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Crystal structure of Glycine Cleavage Protein H-Like (GcvH-L) from Streptococcus pyogenes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ONL PDB ENTRY 1ONL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 2.0 M NAH2PO4/K2HPO4 PH 7.0
Crystal Properties Matthews coefficient Solvent content 4.95 75.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.123 α = 90 b = 64.123 β = 90 c = 73.042 γ = 120
Symmetry Space Group P 31 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 PIXEL DECTRIS PILATUS 2M TORROIDAL MIRROR 2014-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 Diamond I04-1
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 1.5 55.53 99.3 0.04 27.1 8.5 28124
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 1.5 1.53 93 0.57 2.9 6.2
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 1ONL 1.5 55.53 26689 1405 99.22 0.15395 0.15288 0.1636 0.17257 0.1767 RANDOM 23.514
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] 0.1 0.05 0.1 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.907 r_dihedral_angle_4_deg 25.37 r_dihedral_angle_3_deg 10.82 r_long_range_B_refined 9.044 r_long_range_B_other 9.044 r_dihedral_angle_1_deg 7.053 r_scangle_other 5.325 r_scbond_it 3.531 r_scbond_other 3.52 r_mcangle_other 3.147
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.907 r_dihedral_angle_4_deg 25.37 r_dihedral_angle_3_deg 10.82 r_long_range_B_refined 9.044 r_long_range_B_other 9.044 r_dihedral_angle_1_deg 7.053 r_scangle_other 5.325 r_scbond_it 3.531 r_scbond_other 3.52 r_mcangle_other 3.147 r_mcangle_it 3.146 r_mcbond_it 1.96 r_mcbond_other 1.95 r_angle_refined_deg 1.552 r_angle_other_deg 0.768 r_chiral_restr 0.108 r_bond_refined_d 0.021 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 857 Nucleic Acid Atoms Solvent Atoms 250 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing