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Crystal structure of Thermolysin in complex with N-methylurea
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2A7G PDB entry 2A7G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 288 50 mM Tris/HCl, 50 % DMSO, 1.8 M CsCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 2.35 47.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.088 α = 90 b = 93.088 β = 90 c = 129.149 γ = 120
Symmetry Space Group P 61 2 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 IMAGE PLATE MAR scanner 345 mm plate mirrors 2010-03-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OTHER 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.97 25 96.1 0.091 22 7.3 21974 21974
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.97 2 98.3 0.472 3.9 6.5 1143
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 FOURIER SYNTHESIS FREE R PDB entry 2A7G 1.97 10 21974 21974 2167 92.4 0.176 0.176 0.164 0.1766 0.231 0.198 RANDOM
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 2 2246 2620.47
RMS Deviations Key Refinement Restraint Deviation s_similar_adp_cmpnt 0.062 s_non_zero_chiral_vol 0.031 s_zero_chiral_vol 0.028 s_from_restr_planes 0.023 s_angle_d 0.021 s_anti_bump_dis_restr 0.009 s_bond_d 0.005 s_similar_dist s_rigid_bond_adp_cmpnt s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2416 Nucleic Acid Atoms Solvent Atoms 188 Heterogen Atoms 22
Software Software Software Name Purpose SHELXL-97 refinement CNS refinement MAR345dtb data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing