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X-ray crystal structure of Streptococcus sanguinis dimanganese(II)-NrdF
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3N37 PDB ENTRY 3N37
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.6 298 PEG 3000, magnesium formate, pH 7.6, vapor diffusion, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.56 51.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.657 α = 90 b = 80.224 β = 105.91 c = 166.374 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 100 CCD MARRESEARCH 2012-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.078 APS 21-ID-D
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 2.65 29.881 86753
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 3N37 2.65 29.9 75270 3799 86.52 0.2377 0.2355 0.2356 0.2778 0.278 RANDOM 49.4168
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] -1.51 -0.6 1.29 0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.638 r_dihedral_angle_3_deg 14.519 r_dihedral_angle_4_deg 10.274 r_dihedral_angle_1_deg 4.594 r_angle_refined_deg 0.806 r_angle_other_deg 0.677 r_chiral_restr 0.046 r_bond_refined_d 0.005 r_gen_planes_refined 0.002 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.638 r_dihedral_angle_3_deg 14.519 r_dihedral_angle_4_deg 10.274 r_dihedral_angle_1_deg 4.594 r_angle_refined_deg 0.806 r_angle_other_deg 0.677 r_chiral_restr 0.046 r_bond_refined_d 0.005 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18625 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction SCALEPACK data scaling BALBES phasing