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HNL from Hevea brasiliensis to atomic resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QJ4 PDB ENTRY 1QJ4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 2% PEG400, 2M ammonium sulphate, 0.1M Hepes-Na, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.76 55.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.276 α = 90 b = 106.344 β = 90 c = 128.312 γ = 90
Symmetry Space Group C 2 2 21
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 mirrors 2005-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A 0.8550 EMBL/DESY, HAMBURG BW7A
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 1.05 35 100 0.045 35 6.2 145202 145202 -3 -3 8.1
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) 1.05 1.06 90 0.303 4.3 4 3390
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MR/rigid body placement FREE R initially, final refinement against all data PDB ENTRY 1QJ4 1.05 35 145193 145193 100 0.1018 0.0972 RANDOM 12
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 58 2034.91 2610.7
RMS Deviations Key Refinement Restraint Deviation s_anti_bump_dis_restr 0.107 s_approx_iso_adps 0.105 s_non_zero_chiral_vol 0.095 s_zero_chiral_vol 0.092 s_similar_adp_cmpnt 0.04 s_angle_d 0.03 s_from_restr_planes 0.0294 s_bond_d 0.015 s_rigid_bond_adp_cmpnt 0.006 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4567 Nucleic Acid Atoms Solvent Atoms 612 Heterogen Atoms 28
Software Software Software Name Purpose SHELX model building SHELXL-97 refinement MAR345 data collection DENZO data reduction SCALEPACK data scaling REFMAC phasing