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Crystal structure of S213G variant DAH7PS without Tyr bound from Neisseria meningitidis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HSO PDB ENTRY 4HSO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293.15 A protein solution [11 mg/mL in 10 mM BTP buffer (pH 7.3)] was mixed 1:1 (v/v) with a reservoir solution containing 0.2 M trimethylamine N-oxide, 0.1 M Tris (pH 8.5), 15% 20% (w/v) PEG 2000 mme, 0.4 mM MnSO4. The drop sizes were 2 uL, and the volume of the reservoir solution was 500 uL, temperature 293.15K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.33 47.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.064 α = 90 b = 132.432 β = 95.72 c = 75.028 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 210r 2011-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.9537 Australian Synchrotron MX1
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 1.931 74.654 99.4 0.067 15.3 3.8 55141 55141
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 2.4 2.47 99.9 0.486 2.7 3.8 4518
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 4HSO 2.4 19.59 55115 3384 99.25 0.1935 0.1914 0.1952 0.2247 0.2278 RANDOM 48.9273
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] -1.57 -0.05 2.18 -0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.116 r_dihedral_angle_4_deg 17.425 r_dihedral_angle_3_deg 15.357 r_dihedral_angle_1_deg 4.962 r_mcangle_it 2.248 r_angle_refined_deg 1.444 r_mcbond_it 1.397 r_mcbond_other 1.395 r_angle_other_deg 1.24 r_chiral_restr 0.079
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.116 r_dihedral_angle_4_deg 17.425 r_dihedral_angle_3_deg 15.357 r_dihedral_angle_1_deg 4.962 r_mcangle_it 2.248 r_angle_refined_deg 1.444 r_mcbond_it 1.397 r_mcbond_other 1.395 r_angle_other_deg 1.24 r_chiral_restr 0.079 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.006 r_gen_planes_other 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10404 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms 39
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection XSCALE data scaling