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BcSIRED from Bacillus cereus in complex with NADPH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZGY PDB ENTRY 3ZGY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 30% (W/V) PEG 3350; 0.2M MGCL2; 0.1M HEPES PH 7.5; PROTEIN AT 50 MG ML-1
Crystal Properties Matthews coefficient Solvent content 3.2 62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.23 α = 90 b = 62.78 β = 90 c = 214.5 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 PIXEL DECTRIS PILATUS 6M 2014-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
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 1.81 107.25 99.3 0.03 18.8 6.5 69092 2
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 1.81 1.86 99.8 0.63 2.7 6.4
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 PDB ENTRY 3ZGY 1.81 107.25 65636 3365 99.86 0.17356 0.17236 0.1828 0.1966 0.2054 RANDOM 30.734
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] -0.76 2.35 -1.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.722 r_dihedral_angle_4_deg 25.108 r_dihedral_angle_3_deg 15.051 r_dihedral_angle_1_deg 5.687 r_scbond_it 4.433 r_mcangle_it 3.222 r_mcbond_it 2.603 r_mcbond_other 2.595 r_angle_refined_deg 1.998 r_angle_other_deg 1.427
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.722 r_dihedral_angle_4_deg 25.108 r_dihedral_angle_3_deg 15.051 r_dihedral_angle_1_deg 5.687 r_scbond_it 4.433 r_mcangle_it 3.222 r_mcbond_it 2.603 r_mcbond_other 2.595 r_angle_refined_deg 1.998 r_angle_other_deg 1.427 r_chiral_restr 0.158 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 r_bond_other_d 0.006 r_gen_planes_other 0.005 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_mcangle_other 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 4360 Nucleic Acid Atoms Solvent Atoms 355 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement xia2 data reduction SCALA data scaling MOLREP phasing