☰ Navigation Tabs
Crystal structure of Bacillus clausii pdxR at 2.8 Angstroms resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MGR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 291 33% (vol/vol) PEG400, 200 mM calcium acetate, and 200 mM imidazole, pH7.5.
Crystal Properties Matthews coefficient Solvent content 2.81 56.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 250.84 α = 90 b = 250.84 β = 90 c = 370.3 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 PIXEL DECTRIS PILATUS 6M 2015-09-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.8 125.42 98.6 0.999 15.5 25.1 164628
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.87 0.279
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4MGR 2.8 125.735 164628 8331 98.185 0.212 0.2094 0.2094 0.2537 0.2539 111.655
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] 0.324 0.162 0.324 -1.052
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.16 r_dihedral_angle_4_deg 25.421 r_lrange_it 25.167 r_scangle_it 19.728 r_mcangle_it 17.951 r_dihedral_angle_3_deg 17.398 r_scbond_it 14.601 r_mcbond_it 13.007 r_dihedral_angle_1_deg 7.525 r_angle_refined_deg 1.706
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.16 r_dihedral_angle_4_deg 25.421 r_lrange_it 25.167 r_scangle_it 19.728 r_mcangle_it 17.951 r_dihedral_angle_3_deg 17.398 r_scbond_it 14.601 r_mcbond_it 13.007 r_dihedral_angle_1_deg 7.525 r_angle_refined_deg 1.706 r_nbtor_refined 0.32 r_symmetry_nbd_refined 0.298 r_symmetry_xyhbond_nbd_refined 0.242 r_nbd_refined 0.227 r_metal_ion_refined 0.158 r_xyhbond_nbd_refined 0.151 r_chiral_restr 0.128 r_ncsr_local_group_2 0.097 r_ncsr_local_group_1 0.094 r_ncsr_local_group_10 0.094 r_ncsr_local_group_6 0.093 r_ncsr_local_group_22 0.093 r_ncsr_local_group_23 0.093 r_ncsr_local_group_12 0.091 r_ncsr_local_group_41 0.091 r_ncsr_local_group_8 0.09 r_ncsr_local_group_14 0.09 r_ncsr_local_group_18 0.09 r_ncsr_local_group_7 0.088 r_ncsr_local_group_15 0.088 r_ncsr_local_group_24 0.087 r_ncsr_local_group_11 0.086 r_ncsr_local_group_19 0.086 r_ncsr_local_group_20 0.086 r_ncsr_local_group_32 0.086 r_ncsr_local_group_43 0.085 r_ncsr_local_group_3 0.084 r_ncsr_local_group_21 0.084 r_ncsr_local_group_40 0.084 r_ncsr_local_group_4 0.083 r_ncsr_local_group_16 0.083 r_ncsr_local_group_29 0.083 r_ncsr_local_group_5 0.082 r_ncsr_local_group_27 0.082 r_ncsr_local_group_28 0.081 r_ncsr_local_group_36 0.081 r_ncsr_local_group_37 0.081 r_ncsr_local_group_9 0.08 r_ncsr_local_group_33 0.08 r_ncsr_local_group_26 0.079 r_ncsr_local_group_31 0.079 r_ncsr_local_group_42 0.078 r_ncsr_local_group_13 0.077 r_ncsr_local_group_17 0.077 r_ncsr_local_group_38 0.077 r_ncsr_local_group_30 0.076 r_ncsr_local_group_34 0.076 r_ncsr_local_group_44 0.076 r_ncsr_local_group_45 0.074 r_ncsr_local_group_35 0.073 r_ncsr_local_group_25 0.072 r_ncsr_local_group_39 0.069 r_gen_planes_refined 0.009 r_bond_refined_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 30571 Nucleic Acid Atoms Solvent Atoms 90 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MoRDa phasing PARROT phasing DM phasing Coot model building