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X-ray crystal structure of Streptococcus sanguinis NrdIox
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RLJ PDB ENTRY 1RLJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 298 PEG 4000, ammonium sulfate, pH 5.6, vapor diffusion, sitting drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.6 52.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.726 α = 90 b = 56.612 β = 106.13 c = 73.387 γ = 90
Symmetry Space Group C 1 2 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 2012-08-19 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 1.88 50 33395
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 1RLJ 1.88 47.69 33340 1675 99.38 0.2083 0.2067 0.2066 0.2376 0.2349 RANDOM 33.6281
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] 0.49 -0.51 1.5 -2.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.47 r_dihedral_angle_4_deg 18.617 r_dihedral_angle_3_deg 14.528 r_dihedral_angle_1_deg 4.72 r_angle_refined_deg 1.008 r_chiral_restr 0.067 r_bond_refined_d 0.005 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2405 Nucleic Acid Atoms Solvent Atoms 204 Heterogen Atoms 72
Software Software Software Name Purpose SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction