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Crystal structure of MnmE from Chlorobium tepidum in complex with GCP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XZP PDB ENTRY 1XZP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 100mM MES, 46mM NaOH, 12% PEG 4000, 40mM NaCl, 5mM GCP, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.93 68.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.882 α = 90 b = 224.572 β = 90 c = 156.788 γ = 90
Symmetry Space Group C 2 2 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 CCD MAR CCD 165 mm Mirrors 2006-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9796 SLS X10SA
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 3.4 20 99.2 0.129 0.131 12.13 7.45 34300 34042 92.53
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) 3.4 3.425 100 0.654 2.02 7.61 719
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 1XZP 3.4 19.94 32320 1721 99.25 0.24624 0.245 0.2791 0.26891 0.2851 RANDOM 123.559
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] -0.81 -5.79 6.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.351 r_dihedral_angle_3_deg 18.652 r_dihedral_angle_4_deg 17.403 r_dihedral_angle_1_deg 5.607 r_scangle_it 2.106 r_angle_refined_deg 1.198 r_scbond_it 1.144 r_mcangle_it 1.005 r_mcbond_it 0.537 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.351 r_dihedral_angle_3_deg 18.652 r_dihedral_angle_4_deg 17.403 r_dihedral_angle_1_deg 5.607 r_scangle_it 2.106 r_angle_refined_deg 1.198 r_scbond_it 1.144 r_mcangle_it 1.005 r_mcbond_it 0.537 r_nbtor_refined 0.298 r_symmetry_vdw_refined 0.224 r_nbd_refined 0.217 r_symmetry_hbond_refined 0.193 r_xyhbond_nbd_refined 0.125 r_chiral_restr 0.081 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 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 8715 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 65
Software Software Software Name Purpose MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling