4PMJ

Crystal structure of a putative oxidoreductase from Sinorhizobium meliloti 1021 in complex with NADP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72890.2 ul of 14 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG-II condition #42 (1.1 M Ammonium Tartrate Dibasic pH 7.0) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization protein was incubated with 1/50 v/v of 2 mg/ml chymotrypsin solution at 289 K for 3 hours.
Crystal Properties
Matthews coefficientSolvent content
2.2645.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.324α = 90
b = 78.897β = 90
c = 79.563γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2014-03-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.25097.90.1360.13611.461476014450-325.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.2485.70.4571.94.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT2.2501367773197.870.169770.167250.21676RANDOM30.852
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.021-1.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.145
r_dihedral_angle_3_deg14.328
r_dihedral_angle_4_deg12.063
r_dihedral_angle_1_deg5.768
r_long_range_B_refined5.72
r_long_range_B_other5.719
r_scangle_other2.005
r_angle_refined_deg1.662
r_scbond_it1.304
r_scbond_other1.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.145
r_dihedral_angle_3_deg14.328
r_dihedral_angle_4_deg12.063
r_dihedral_angle_1_deg5.768
r_long_range_B_refined5.72
r_long_range_B_other5.719
r_scangle_other2.005
r_angle_refined_deg1.662
r_scbond_it1.304
r_scbond_other1.301
r_mcangle_other1.258
r_mcangle_it1.257
r_angle_other_deg0.947
r_mcbond_it0.749
r_mcbond_other0.745
r_chiral_restr0.09
r_bond_refined_d0.013
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2127
Nucleic Acid Atoms
Solvent Atoms115
Heterogen Atoms54

Software

Software
Software NamePurpose
HKL-3000data collection
HKL-3000phasing
HKL-3000data scaling
SHELXDEphasing
MLPHAREphasing
DMphasing
Cootmodel building
REFMACrefinement
PDB_EXTRACTdata extraction