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Periplasmic heme-binding protein RhuT from Roseiflexus sp. RS-1 in two-heme bound form (holo-2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MD9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6 293 5% PEG 8000, 0.1 M zinc acetate, and 50 mM MES
Crystal Properties Matthews coefficient Solvent content 3.06 59.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.326 α = 90 b = 86.338 β = 90 c = 118.806 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 RAYONIX MX225-HS mirrors 2015-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1.00 SPring-8 BL32XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 50 99.8 0.114 8.1 7.9 23911
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) 1 2 2.03 97.8 0.544 7.1
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 3MD9 2 43.21 21312 1157 94.42 0.1892 0.1873 0.1864 0.2243 0.2254 RANDOM 26.41
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] 0.4 -0.23 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.282 r_dihedral_angle_4_deg 22.068 r_dihedral_angle_3_deg 13.609 r_dihedral_angle_1_deg 5.651 r_angle_refined_deg 1.831 r_chiral_restr 0.145 r_bond_refined_d 0.016 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1987 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms 90
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction