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crystal structure of Oxidized MerP from Ralstonia metallidurans CH34
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AFI PDB entry 1AFI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 PEGMME5000, Sodium acetate, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.03 39.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.81 α = 90 b = 52.612 β = 90 c = 60.006 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 MARRESEARCH osmic multi-layer mirror M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR591 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 40 97 0.054 0.048 10.7 4.2 9437 1 35
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.05 97 0.335 0.282 2.1 3.7 655
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 (All) 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 1AFI 2 39.53 8498 938 96.1 0.19976 0.1997 0.1923 0.2015 0.26754 0.2785 RANDOM 33.569
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] -0.08 0.28 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.136 r_scangle_it 5.797 r_scbond_it 3.593 r_angle_refined_deg 2.306 r_mcangle_it 2.273 r_mcbond_it 1.484 r_angle_other_deg 1.213 r_symmetry_vdw_other 0.288 r_nbd_other 0.255 r_symmetry_vdw_refined 0.215
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.136 r_scangle_it 5.797 r_scbond_it 3.593 r_angle_refined_deg 2.306 r_mcangle_it 2.273 r_mcbond_it 1.484 r_angle_other_deg 1.213 r_symmetry_vdw_other 0.288 r_nbd_other 0.255 r_symmetry_vdw_refined 0.215 r_nbd_refined 0.214 r_xyhbond_nbd_refined 0.179 r_chiral_restr 0.148 r_symmetry_hbond_refined 0.148 r_nbtor_other 0.091 r_bond_refined_d 0.034 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1090 Nucleic Acid Atoms Solvent Atoms 125 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction CCP4 data scaling BEAST phasing