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Crystal structure of Magnetospirillum gryphiswaldense MSR-1 holo-Fur
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RAY PDB entry 4RAY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 277 pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.47 64.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.595 α = 90 b = 96.847 β = 90 c = 119.874 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 130 CCD ADSC QUANTUM 315 2012-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 1.0 SSRF BL17U
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 1.9 50 99.5 36939 36732 3 3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.93 95.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 4RAY 1.9 50 3 36732 34732 1832 99.15 0.20405 0.20281 0.2004 0.22729 0.2247 RANDOM 34.471
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] 2.38 -0.88 -1.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.475 r_dihedral_angle_4_deg 16.008 r_dihedral_angle_3_deg 14.249 r_dihedral_angle_1_deg 5.568 r_angle_refined_deg 1.293 r_chiral_restr 0.089 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.475 r_dihedral_angle_4_deg 16.008 r_dihedral_angle_3_deg 14.249 r_dihedral_angle_1_deg 5.568 r_angle_refined_deg 1.293 r_chiral_restr 0.089 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined 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 2174 Nucleic Acid Atoms Solvent Atoms 190 Heterogen Atoms 16
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling