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The mutant G127C-T313C of Deinococcus Radiodurans N-acylamino acid racemase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R0M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 lithium sulfate, Tris-HCl, PEG4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.47 50.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.129 α = 90 b = 116.129 β = 90 c = 120.536 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 113 IMAGE PLATE RIGAKU RAXIS IV 2004-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 30 97.1 107937
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 2.07 95.3
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 1R0M 2 30 99316 5219 97.07 0.18427 0.18202 0.1864 0.22715 0.182 RANDOM 20.159
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] 0.32 0.32 -0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.191 r_dihedral_angle_4_deg 20.06 r_dihedral_angle_3_deg 14.109 r_dihedral_angle_1_deg 5.952 r_scangle_it 2.018 r_mcangle_it 1.683 r_angle_refined_deg 1.299 r_scbond_it 1.285 r_mcbond_it 1.113 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.191 r_dihedral_angle_4_deg 20.06 r_dihedral_angle_3_deg 14.109 r_dihedral_angle_1_deg 5.952 r_scangle_it 2.018 r_mcangle_it 1.683 r_angle_refined_deg 1.299 r_scbond_it 1.285 r_mcbond_it 1.113 r_nbtor_refined 0.31 r_nbd_refined 0.21 r_symmetry_hbond_refined 0.204 r_xyhbond_nbd_refined 0.173 r_symmetry_vdw_refined 0.166 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11068 Nucleic Acid Atoms Solvent Atoms 891 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing