1W61

proline racemase in complex with 2 molecules of pyrrole-2-carboxylic acid (holo form)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherMODEL OF THE SAME PROTEIN OBTAINED BY SAD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.615% PEG 4000,100MM NH4ACETATE 50MM NA3CITRATE.2H2O,PH5.6, pH 5.60
Crystal Properties
Matthews coefficientSolvent content
2.550.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 131.153α = 90
b = 91.209β = 126.52
c = 85.983γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC CCDTOROIDAL MIRRORMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

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
12.169.298.80.0715.43.746967223.92
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)
12.12.2194.10.137.73.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTMODEL OF THE SAME PROTEIN OBTAINED BY SAD2.13046958233198.80.150.1480.193RANDOM22.6
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]
1.4250.727-0.7440.183
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.855
r_dihedral_angle_3_deg15.406
r_dihedral_angle_4_deg13.61
r_dihedral_angle_1_deg6.9
r_scangle_it4.239
r_scbond_it3.014
r_mcbond_it1.778
r_angle_refined_deg1.72
r_mcangle_it1.696
r_angle_other_deg0.886
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.855
r_dihedral_angle_3_deg15.406
r_dihedral_angle_4_deg13.61
r_dihedral_angle_1_deg6.9
r_scangle_it4.239
r_scbond_it3.014
r_mcbond_it1.778
r_angle_refined_deg1.72
r_mcangle_it1.696
r_angle_other_deg0.886
r_symmetry_vdw_refined0.346
r_symmetry_vdw_other0.289
r_symmetry_hbond_refined0.227
r_nbd_other0.198
r_nbd_refined0.195
r_nbtor_refined0.175
r_xyhbond_nbd_refined0.144
r_chiral_restr0.108
r_nbtor_other0.091
r_bond_refined_d0.019
r_gen_planes_refined0.007
r_bond_other_d0.006
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5374
Nucleic Acid Atoms
Solvent Atoms358
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing