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Streptococcus pyogenes Dpr
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UMN PDB ENTRY 1UMN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 0.1M HEPES PH 7.0, 1M SUCCINIC ACID PH 7.0, 1% W/V PEG 2000 MME, 5% 2-PROPANOL
Crystal Properties Matthews coefficient Solvent content 3.2 62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 189.268 α = 90 b = 189.268 β = 90 c = 189.268 γ = 90
Symmetry Space Group F 41 3 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 CCD MARRESEARCH BENT, VERTICALLY FOCUSSING 2009-02-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 EMBL/DESY, HAMBURG X13
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 2 33 99.9 0.15 10.8 6.3 20144 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 2 2.11 100 0.49 3.5 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 1UMN 2 33 19097 1025 99.75 0.15443 0.15296 0.1541 0.18198 0.1834 RANDOM 15.065
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.335 r_dihedral_angle_4_deg 22.434 r_dihedral_angle_3_deg 11.641 r_dihedral_angle_1_deg 4.269 r_scangle_it 2.814 r_scbond_it 1.648 r_angle_refined_deg 0.987 r_mcangle_it 0.98 r_mcbond_it 0.508 r_chiral_restr 0.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.335 r_dihedral_angle_4_deg 22.434 r_dihedral_angle_3_deg 11.641 r_dihedral_angle_1_deg 4.269 r_scangle_it 2.814 r_scbond_it 1.648 r_angle_refined_deg 0.987 r_mcangle_it 0.98 r_mcbond_it 0.508 r_chiral_restr 0.072 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other 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 1291 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing