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Crystal structure of putative mandelate racemase from Bordetella bronchiseptica RB50 complexed with 2-oxoglutarate/phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3H12
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 2.8 M sodium acetate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.42 49.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.55 α = 90 b = 117.55 β = 90 c = 123.21 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2010-08-19 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.075 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2 50 99.9 0.111 7.6 7.6 56531
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.03 99.7 6.6 2806
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3H12 2 19.99 47085 2389 83.97 0.1854 0.1834 0.1894 0.2223 0.2319 RANDOM 32.063
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.168 r_dihedral_angle_4_deg 15.433 r_dihedral_angle_3_deg 14.279 r_scbond_it 8.287 r_dihedral_angle_1_deg 5.934 r_mcangle_it 3.36 r_angle_refined_deg 1.173 r_mcbond_it 0.884 r_scangle_it 0.836 r_chiral_restr 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.168 r_dihedral_angle_4_deg 15.433 r_dihedral_angle_3_deg 14.279 r_scbond_it 8.287 r_dihedral_angle_1_deg 5.934 r_mcangle_it 3.36 r_angle_refined_deg 1.173 r_mcbond_it 0.884 r_scangle_it 0.836 r_chiral_restr 0.08 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5728 Nucleic Acid Atoms Solvent Atoms 403 Heterogen Atoms 17
Software Software Software Name Purpose SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CBASS data collection HKL-2000 data reduction