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The crystal structure of Bacillus subtilis YpgQ in complex with ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DQV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 291 40% PEG 600, 0.1 M sodium citrate
Crystal Properties Matthews coefficient Solvent content 2.14 42.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.865 α = 90 b = 52.499 β = 93.33 c = 82.322 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 ADSC QUANTUM 270 2014-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 1.00004 PAL/PLS 7A (6B, 6C1)
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 2.15 30 99.6 34 3.7 22139
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 2.15 2.23 100 0.441 3.7 3.7
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 5DQV 2.15 30 20727 1118 99.5 0.21209 0.20939 0.2113 0.26134 0.2579 RANDOM 53.5
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] -2.04 -1.63 3.19 -1.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.262 r_dihedral_angle_4_deg 22.924 r_dihedral_angle_3_deg 13.609 r_dihedral_angle_1_deg 5.289 r_angle_other_deg 4.35 r_scangle_it 3.117 r_scbond_it 1.966 r_angle_refined_deg 1.342 r_mcangle_it 1.087 r_mcbond_it 0.611
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.262 r_dihedral_angle_4_deg 22.924 r_dihedral_angle_3_deg 13.609 r_dihedral_angle_1_deg 5.289 r_angle_other_deg 4.35 r_scangle_it 3.117 r_scbond_it 1.966 r_angle_refined_deg 1.342 r_mcangle_it 1.087 r_mcbond_it 0.611 r_chiral_restr 0.081 r_bond_refined_d 0.014 r_gen_planes_other 0.007 r_gen_planes_refined 0.005 r_bond_other_d 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 2836 Nucleic Acid Atoms Solvent Atoms 46 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing