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NvPizza2-H16S58 with cobalt
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WW7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 unbuffered 1.7 M ammonium sulphate, 10 mM cobalt chloride
Crystal Properties Matthews coefficient Solvent content 2.47 50.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.453 α = 90 b = 69.453 β = 90 c = 187.264 γ = 120
Symmetry Space Group P 61 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 100 CCD MARMOSAIC 225 mm CCD 2015-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.00 SPring-8 BL26B1
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 1.95 43.3 96.7 0.055 29.4 9.7 19759
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 1.95 1.98 88.4 0.289 3.3 3
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 3WW7 1.95 43.3 18743 999 96.96 0.20529 0.20233 0.2081 0.26207 0.2694 RANDOM 39.058
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] 0.34 0.17 0.34 -1.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.697 r_dihedral_angle_4_deg 18.545 r_dihedral_angle_3_deg 13.227 r_long_range_B_refined 7.9 r_long_range_B_other 7.877 r_dihedral_angle_1_deg 7.735 r_scangle_other 5.729 r_mcangle_it 5.581 r_mcangle_other 5.58 r_scbond_it 4.073
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.697 r_dihedral_angle_4_deg 18.545 r_dihedral_angle_3_deg 13.227 r_long_range_B_refined 7.9 r_long_range_B_other 7.877 r_dihedral_angle_1_deg 7.735 r_scangle_other 5.729 r_mcangle_it 5.581 r_mcangle_other 5.58 r_scbond_it 4.073 r_scbond_other 4.032 r_mcbond_it 3.682 r_mcbond_other 3.68 r_angle_refined_deg 1.977 r_angle_other_deg 1.022 r_chiral_restr 0.102 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.002 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 1842 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing