3DM8

Crystal Structure of Putative Isomerase from Rhodopseudomonas palustris


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.5294PEG400 15%, MgCl2 0.2M, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.5351.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.593α = 90
b = 84.071β = 90
c = 97.211γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDAPS-1MIRROR2007-02-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.97912APS19-BM

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
11.848.6299.90.0570.057357.51587015870-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8696.30.3220.3226.27.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSIR/SIRASTHROUGHOUT1.848.6215828158287900.180.180.1780.216RANDOM15.62
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]
-0.080.32-0.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.408
r_dihedral_angle_4_deg17.454
r_dihedral_angle_3_deg15.818
r_dihedral_angle_1_deg6.437
r_scangle_it5.083
r_scbond_it3.237
r_mcangle_it1.868
r_angle_refined_deg1.705
r_angle_other_deg1.428
r_mcbond_it1.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.408
r_dihedral_angle_4_deg17.454
r_dihedral_angle_3_deg15.818
r_dihedral_angle_1_deg6.437
r_scangle_it5.083
r_scbond_it3.237
r_mcangle_it1.868
r_angle_refined_deg1.705
r_angle_other_deg1.428
r_mcbond_it1.001
r_mcbond_other0.333
r_chiral_restr0.109
r_bond_refined_d0.019
r_gen_planes_refined0.008
r_gen_planes_other0.002
r_bond_other_d0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1079
Nucleic Acid Atoms
Solvent Atoms174
Heterogen Atoms12

Software

Software
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-3000phasing
MLPHAREphasing
DMmodel building
SHELXDphasing
ARP/wARPmodel building
Cootmodel building
REFMACrefinement
HKL-2000data scaling
DMphasing