4MLV

Crystal Structure of Bacillus megaterium porphobilinogen deaminase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PDAPDB ENTRY 1PDA

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
2.4750.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.32α = 90
b = 65.78β = 90
c = 97.21γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2013-03-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.976DiamondI03

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
11.45548.61000.06114.46.26077260772
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)
11.4551.531000.55936

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUTPDB ENTRY 1PDA1.45546.756077257626307399.980.143310.141120.18559RANDOM23.972
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]
-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.127
r_sphericity_free25.619
r_dihedral_angle_4_deg22.985
r_dihedral_angle_3_deg13.854
r_sphericity_bonded11.816
r_rigid_bond_restr8.154
r_dihedral_angle_1_deg6.369
r_scbond_other5.689
r_scbond_it5.685
r_scangle_other5.589
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.127
r_sphericity_free25.619
r_dihedral_angle_4_deg22.985
r_dihedral_angle_3_deg13.854
r_sphericity_bonded11.816
r_rigid_bond_restr8.154
r_dihedral_angle_1_deg6.369
r_scbond_other5.689
r_scbond_it5.685
r_scangle_other5.589
r_long_range_B_refined4.98
r_long_range_B_other4.808
r_mcangle_other3.331
r_mcangle_it3.325
r_mcbond_it2.796
r_mcbond_other2.734
r_angle_refined_deg2.438
r_angle_other_deg2.208
r_chiral_restr0.158
r_bond_refined_d0.024
r_gen_planes_refined0.012
r_bond_other_d0.005
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 Atoms2253
Nucleic Acid Atoms
Solvent Atoms325
Heterogen Atoms65

Software

Software
Software NamePurpose
GDAdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling