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High-resolution structure of the Ni-bound form of the Y135F mutant of C. metallidurans CnrXs
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Y39
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 PEG 3350, HEPES, sodium/potassium phosphate
Crystal Properties Matthews coefficient Solvent content 1.93 36.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.401 α = 90 b = 32.401 β = 90 c = 195.331 γ = 90
Symmetry Space Group P 41 21 2
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 315r 2013-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.979725 ESRF BM30A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.107 39.066 98.9 0.089 0.103 0.036 16.6 8.4 42671 42671
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.11 1.17 96.4 0.333 0.333 0.13 2.2 8.1 5927
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 2Y39 1.11 30 40322 1980 98.8 0.109 0.1083 0.1088 0.1237 0.1238 RANDOM 8.822
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] -0.02 -0.02 0.04
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 25.873 r_dihedral_angle_2_deg 25.767 r_dihedral_angle_4_deg 20.283 r_dihedral_angle_3_deg 11.916 r_sphericity_bonded 9.474 r_dihedral_angle_1_deg 4.28 r_rigid_bond_restr 2.926 r_angle_refined_deg 1.678 r_mcangle_it 1.377 r_mcbond_it 1.155
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 25.873 r_dihedral_angle_2_deg 25.767 r_dihedral_angle_4_deg 20.283 r_dihedral_angle_3_deg 11.916 r_sphericity_bonded 9.474 r_dihedral_angle_1_deg 4.28 r_rigid_bond_restr 2.926 r_angle_refined_deg 1.678 r_mcangle_it 1.377 r_mcbond_it 1.155 r_mcbond_other 1.155 r_angle_other_deg 0.794 r_chiral_restr 0.088 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 887 Nucleic Acid Atoms Solvent Atoms 260 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction