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Structure of haloalkane dehalogenase DhaA14 mutant I135F from Rhodococcus rhodochrous
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BN6 PDB ENTRY 1BN6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 9 277 [protein]=7-10 mg/ml in 50mM Tris-HCl buffer pH 7.5;
[Precipitant]=25% PEG 4000, 8% 2-propanol in 100mM sodium acetate., VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.14 40.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.73 α = 115.5 b = 44.44 β = 97.87 c = 46.63 γ = 109.52
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 MAR CCD 165 mm 2007-08-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 EMBL/DESY, HAMBURG X11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 0.95 30 94.2 0.059 0.059 26.4 5.8 163495 7.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.95 0.97 90.6 0.418 0.418 4.4 4
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 MOLECULAR REPLACEMENT FREE R PDB ENTRY 1BN6 0.95 10 163371 163371 8179 94.2 0.1149 0.1149 0.1149 0.1243 0.1374 0.1292 RANDOM 8.763
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] 0.14 0.14 0.41 0.03 0.3 0.3
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 64 2132.7 2881.55
RMS Deviations Key Refinement Restraint Deviation s_zero_chiral_vol 0.104 s_non_zero_chiral_vol 0.1 s_anti_bump_dis_restr 0.036 s_similar_adp_cmpnt 0.033 s_angle_d 0.031 s_from_restr_planes 0.0283 s_bond_d 0.015 s_rigid_bond_adp_cmpnt 0.005 s_similar_dist s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2372 Nucleic Acid Atoms Solvent Atoms 520 Heterogen Atoms 9
Software Software Software Name Purpose SHELXL-97 refinement MOLREP phasing REFMAC refinement Coot model building MolProbity model building DENZO data reduction SCALEPACK data scaling HKL-2000 data collection