4MLQ

Crystal structure of Bacillus megaterium porphobilinogen deaminase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2980.1M sodium cacodylate, 0.2M magnesium acetate, 25-30% PEG 8K, pH 6.5 - 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.4249.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.01α = 90
b = 65.12β = 90
c = 96.78γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2013-04-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM141.072ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.631.3395.60.08810.16.44286642866
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)
11.61.6988.71.4930.94.5

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.631.334272840552217695.050.164620.160610.24215RANDOM28.019
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]
-0.160.47-0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free39.063
r_dihedral_angle_2_deg35.539
r_dihedral_angle_4_deg22.7
r_sphericity_bonded19.976
r_dihedral_angle_3_deg15.1
r_scangle_other8.648
r_long_range_B_refined8.563
r_long_range_B_other8.56
r_scbond_it7.874
r_scbond_other7.871
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free39.063
r_dihedral_angle_2_deg35.539
r_dihedral_angle_4_deg22.7
r_sphericity_bonded19.976
r_dihedral_angle_3_deg15.1
r_scangle_other8.648
r_long_range_B_refined8.563
r_long_range_B_other8.56
r_scbond_it7.874
r_scbond_other7.871
r_mcangle_other6.968
r_mcangle_it6.947
r_dihedral_angle_1_deg6.18
r_mcbond_it5.839
r_mcbond_other5.828
r_rigid_bond_restr5.224
r_angle_refined_deg2.142
r_angle_other_deg1.526
r_chiral_restr0.121
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d0.004
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2245
Nucleic Acid Atoms
Solvent Atoms249
Heterogen Atoms65

Software

Software
Software NamePurpose
MxCuBEdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling