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Crystal structure of a cupin protein (tm1459) in osmium (Os) substituted form I
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VJ2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 25% w/v polyethylene glycol 1500, 0.1M MES
Crystal Properties Matthews coefficient Solvent content 1.84 36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.396 α = 69.07 b = 48.878 β = 87.95 c = 62.597 γ = 78.89
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 RAYONIX MX300HE 2015-05-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
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 1.12 50 94.8 0.087 18.8 3.7 147917
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.12 1.14 91.8 0.44 0.847 2.7 4
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 FREE R-VALUE 1vj2 1.12 50 137888 7237 94.8 0.1514 0.1513 0.1426 0.1798 0.1762 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 169 3943.2
RMS Deviations Key Refinement Restraint Deviation s_non_zero_chiral_vol 0.54 s_zero_chiral_vol 0.09 s_approx_iso_adps 0.0673 s_similar_adp_cmpnt 0.0286 s_rigid_bond_adp_cmpnt 0.0181 s_angle_d 0.0159 s_anti_bump_dis_restr 0.0135 s_bond_d 0.0046 s_from_restr_planes 0.0013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3718 Nucleic Acid Atoms Solvent Atoms 520 Heterogen Atoms 36
Software Software Software Name Purpose PHASER phasing HKL-2000 data reduction HKL-2000 data scaling SHELX phasing SHELXL-97 refinement