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alanine racemase [Clostridium difficile 630]
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4A3Q PDB ENTRY 4A3Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 298 20 mg/ml protein in 50mM Tris pH 8.0, 0.02% v/v BME, 10 micromolar pyridoxal-L-phosphate, crystallization buffer 1mM TCEP, 0.2M sodium formate, 20% w/V PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.44 49.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.15 α = 90 b = 93.3 β = 91 c = 107.09 γ = 90
Symmetry Space Group P 1 21 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 IMAGE PLATE RIGAKU RAXIS HTC 2012-09-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT
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 2.076 54.54 88.4 0.06 19.5 7.5 93251 2
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 2.076 2.2 52.9 0.374 4.9 7
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 PDB ENTRY 4A3Q 2.1 54.54 88493 4555 95.11 0.20478 0.20156 0.215 0.26571 0.264 RANDOM 39.958
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] -0.04 -0.27 0.04 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.591 r_dihedral_angle_4_deg 21.082 r_long_range_B_refined 7.174 r_mcangle_it 5.083 r_scbond_it 4.655 r_mcbond_it 3.792 r_angle_refined_deg 2.014 r_chiral_restr 0.127 r_bond_refined_d 0.018 r_gen_planes_refined 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.591 r_dihedral_angle_4_deg 21.082 r_long_range_B_refined 7.174 r_mcangle_it 5.083 r_scbond_it 4.655 r_mcbond_it 3.792 r_angle_refined_deg 2.014 r_chiral_restr 0.127 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_dihedral_angle_1_deg r_dihedral_angle_3_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11888 Nucleic Acid Atoms Solvent Atoms 568 Heterogen Atoms 22
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling