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Chlamydia trachomatis NrdB with a Mn/Fe cofactor (procedure 1 - high Mn)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SYY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.6 298 PEG 3000, sodium acetate, pH 7.6, vapor diffusion, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.14 42.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.221 α = 90 b = 97.998 β = 97.79 c = 100.291 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.85, 1.72 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 2.2 50 72917
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 1SYY 2.2 29.66 72748 3666 99.39 0.1881 0.1856 0.1844 0.235 0.2351 RANDOM 27.0097
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] -0.44 0.03 0.37 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.986 r_dihedral_angle_4_deg 14.795 r_dihedral_angle_3_deg 14.156 r_dihedral_angle_1_deg 4.791 r_scangle_it 2.164 r_scbond_it 1.247 r_angle_refined_deg 1.002 r_mcangle_it 0.785 r_mcbond_it 0.392 r_chiral_restr 0.077
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.986 r_dihedral_angle_4_deg 14.795 r_dihedral_angle_3_deg 14.156 r_dihedral_angle_1_deg 4.791 r_scangle_it 2.164 r_scbond_it 1.247 r_angle_refined_deg 1.002 r_mcangle_it 0.785 r_mcbond_it 0.392 r_chiral_restr 0.077 r_bond_refined_d 0.008 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10802 Nucleic Acid Atoms Solvent Atoms 527 Heterogen Atoms 24
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction