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alanine racemase [Clostridium difficile 630] complex with cycloserine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LUS PDB ENTRY 4LUS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 20mg/ml protein in 50mM Tris pH 8.0, 0.02% v/v BME, 10 micromolar pyridoxal-L-phosphate, crystallization buffer 0.1M cycloserine, 0.2M sodium formate, 20% w/V PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.36 63.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.84 α = 90 b = 138.97 β = 90 c = 144.89 γ = 90
Symmetry Space Group P 21 21 21
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 2012-10-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.514179
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 2.26 53.72 64.8 0.13 8.7 5.7 30908 35794 2 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 2.26 2.33 55.5 0.893 1.8 5.5 2605
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 4LUS 2.26 45.62 33808 1785 63.97 0.21198 0.21014 0.2236 0.24788 0.2591 RANDOM 33.349
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] -1.64 1.24 0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.631 r_dihedral_angle_4_deg 17.405 r_dihedral_angle_3_deg 16.348 r_long_range_B_refined 6.404 r_dihedral_angle_1_deg 5.889 r_mcangle_it 2.473 r_scbond_it 2.227 r_mcbond_it 1.575 r_mcbond_other 1.571 r_angle_refined_deg 1.352
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.631 r_dihedral_angle_4_deg 17.405 r_dihedral_angle_3_deg 16.348 r_long_range_B_refined 6.404 r_dihedral_angle_1_deg 5.889 r_mcangle_it 2.473 r_scbond_it 2.227 r_mcbond_it 1.575 r_mcbond_other 1.571 r_angle_refined_deg 1.352 r_angle_other_deg 0.977 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.002 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_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 5846 Nucleic Acid Atoms Solvent Atoms 171 Heterogen Atoms 44
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling