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Crystal structure of alanine racemase from Bartonella henselae with covalently bound pyridoxal phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DY3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 289 Native crystal grown in 0.1 M Hepes pH 8.0, 33% PEG 3350 at 42.3 mg/mL, crystal tracking ID 203636d11; crystal used for combined Phaser MR/IodoSAD grown in 0.1 M Hepes pH 8.5, 0.2 M MgCl2, 25% PEG 3350 and soaked for 1 hour in 0.1 M Hepes pH 8.0, 1.0 M KI, 35% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.22 44.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.794 α = 90 b = 54.316 β = 112.39 c = 107.476 γ = 90
Symmetry Space Group C 1 2 1
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 2009-07-11 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD RIGAKU SATURN 944+ 2009-11-16 M SINGLE WAVELENGTH 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.976484 ALS 5.0.3 2 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 2.04 50 99.5 0.088 17.4 5.3 45971
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1,2 2.04 2.12 96.7 0.496 2.79 4.6 4405
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 SAD, MR THROUGHOUT 2DY3 2.04 34.9 45875 2318 98.54 0.193 0.191 0.1934 0.233 0.2352 RANDOM 22.817
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] -0.82 -1.88 -1.01 0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.335 r_dihedral_angle_4_deg 16.392 r_dihedral_angle_3_deg 15.135 r_dihedral_angle_1_deg 6.391 r_scangle_it 3.061 r_scbond_it 1.954 r_angle_refined_deg 1.408 r_mcangle_it 1.167 r_mcbond_it 0.664 r_chiral_restr 0.088
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.335 r_dihedral_angle_4_deg 16.392 r_dihedral_angle_3_deg 15.135 r_dihedral_angle_1_deg 6.391 r_scangle_it 3.061 r_scbond_it 1.954 r_angle_refined_deg 1.408 r_mcangle_it 1.167 r_mcbond_it 0.664 r_chiral_restr 0.088 r_bond_refined_d 0.014 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5407 Nucleic Acid Atoms Solvent Atoms 426 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing SHELX phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling SHELXD phasing