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Crystal structure of Pseudomonas Fluorescens alanine racemase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RCQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.87 57.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 186.739 α = 90 b = 186.739 β = 90 c = 103.657 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 298 IMAGE PLATE RIGAKU RAXIS V mirrors M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 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 2.8 50 93.7 0.085 5.4 3.5 41244 1
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 2.8 2.9 61.4 0.318 1.9 2683
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1RCQ 2.8 46.32 1 41244 39114 2076 93.53 0.2159 0.21431 0.24659 0.2077 RANDOM 53.213
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] -0.14 -0.14 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.168 r_dihedral_angle_4_deg 16.084 r_dihedral_angle_3_deg 14.926 r_dihedral_angle_1_deg 4.877 r_angle_refined_deg 1.046 r_scangle_it 0.476 r_mcangle_it 0.36 r_nbtor_refined 0.293 r_scbond_it 0.262 r_symmetry_hbond_refined 0.251
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.168 r_dihedral_angle_4_deg 16.084 r_dihedral_angle_3_deg 14.926 r_dihedral_angle_1_deg 4.877 r_angle_refined_deg 1.046 r_scangle_it 0.476 r_mcangle_it 0.36 r_nbtor_refined 0.293 r_scbond_it 0.262 r_symmetry_hbond_refined 0.251 r_mcbond_it 0.199 r_nbd_refined 0.159 r_symmetry_vdw_refined 0.099 r_xyhbond_nbd_refined 0.09 r_chiral_restr 0.087 r_bond_refined_d 0.006 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11000 Nucleic Acid Atoms Solvent Atoms 58 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing