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Crystal structure of MnCO/apo-R52CFr
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DAT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 1M ammonium sulfate, 20mM cadmium sulfite
Crystal Properties Matthews coefficient Solvent content 3.15 61.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.733 α = 90 b = 181.733 β = 90 c = 181.733 γ = 90
Symmetry Space Group F 4 3 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 RAYONIX MX225HE 2014-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE SPRING-8 BEAMLINE BL38B1 1.00 SPring-8 BL38B1
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 1.42 27.71 99.8 60.7 20.6 48815
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 1.42 1.44 99.78 0.071 60.7 11
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 1DAT 1.42 27.71 46289 2472 99.78 0.16682 0.1663 0.167 0.1765 0.1785 RANDOM 14.776
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.454 r_dihedral_angle_3_deg 13.283 r_dihedral_angle_4_deg 13.03 r_long_range_B_refined 6.175 r_long_range_B_other 5.92 r_dihedral_angle_1_deg 4.857 r_scangle_other 4.74 r_scbond_it 3.28 r_scbond_other 3.266 r_angle_refined_deg 2.815
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.454 r_dihedral_angle_3_deg 13.283 r_dihedral_angle_4_deg 13.03 r_long_range_B_refined 6.175 r_long_range_B_other 5.92 r_dihedral_angle_1_deg 4.857 r_scangle_other 4.74 r_scbond_it 3.28 r_scbond_other 3.266 r_angle_refined_deg 2.815 r_mcangle_it 2.639 r_mcangle_other 2.638 r_mcbond_it 2.027 r_mcbond_other 1.999 r_angle_other_deg 1.016 r_chiral_restr 0.147 r_bond_refined_d 0.031 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1392 Nucleic Acid Atoms Solvent Atoms 176 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement Coot model building DENZO data reduction SCALEPACK data scaling