9I2V | pdb_00009i2v

Alpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis in complex with fenoprofenoyl-CoA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8RMW 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7295.154 M ammonium acetate, 0.1 M Bis-Trispropane, pH 7.0
Crystal Properties
Matthews coefficientSolvent content
4.0469.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 276.731α = 90
b = 276.731β = 90
c = 390.112γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2024-02-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.953731DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)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
12.07225.711000.1930.0370.9991427.6451154
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
111.34225.7199.90.0310.00617125.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2.07196.4474511172221799.9910.210.20780.21740.24830.257746.296
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]
-0.18-0.180.361
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.901
r_dihedral_angle_6_deg15.408
r_dihedral_angle_2_deg9.597
r_lrange_other8.863
r_lrange_it8.856
r_dihedral_angle_1_deg7.072
r_scangle_it6.855
r_scangle_other6.855
r_mcangle_it6.618
r_mcangle_other6.618
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.901
r_dihedral_angle_6_deg15.408
r_dihedral_angle_2_deg9.597
r_lrange_other8.863
r_lrange_it8.856
r_dihedral_angle_1_deg7.072
r_scangle_it6.855
r_scangle_other6.855
r_mcangle_it6.618
r_mcangle_other6.618
r_scbond_it4.635
r_scbond_other4.635
r_mcbond_it4.625
r_mcbond_other4.625
r_dihedral_angle_other_2_deg3.261
r_angle_refined_deg1.619
r_angle_other_deg0.503
r_nbd_refined0.227
r_symmetry_nbd_other0.196
r_nbtor_refined0.183
r_xyhbond_nbd_refined0.166
r_symmetry_nbd_refined0.158
r_nbd_other0.155
r_symmetry_xyhbond_nbd_refined0.148
r_symmetry_xyhbond_nbd_other0.109
r_symmetry_nbtor_other0.083
r_chiral_restr0.073
r_bond_refined_d0.008
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms32447
Nucleic Acid Atoms
Solvent Atoms1403
Heterogen Atoms780

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building