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Vall from streptomyces hygroscopicus in apo form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3T7D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.02 39.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.671 α = 90 b = 46.693 β = 108.08 c = 123.879 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 2011-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9795 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 1.7 40.965 90507
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 3T7D 1.7 40.39 90507 4761 97.59 0.18061 0.17912 0.1976 0.20921 0.2243 RANDOM 16.798
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] -0.02 0.07 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.831 r_dihedral_angle_4_deg 16.662 r_dihedral_angle_3_deg 13.443 r_dihedral_angle_1_deg 5.544 r_scangle_it 3.279 r_scbond_it 1.983 r_angle_refined_deg 1.221 r_mcangle_it 1.121 r_mcbond_it 0.576 r_chiral_restr 0.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.831 r_dihedral_angle_4_deg 16.662 r_dihedral_angle_3_deg 13.443 r_dihedral_angle_1_deg 5.544 r_scangle_it 3.279 r_scbond_it 1.983 r_angle_refined_deg 1.221 r_mcangle_it 1.121 r_mcbond_it 0.576 r_chiral_restr 0.082 r_bond_refined_d 0.009 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7387 Nucleic Acid Atoms Solvent Atoms 828 Heterogen Atoms 18
Software Software Software Name Purpose HKL-2000 data collection CNS refinement REFMAC refinement HKL-2000 data reduction SCALA data scaling CNS phasing