☰ Navigation Tabs
Crystal structure of a cupin protein (tm1459) in copper (Cu) substituted form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5WSD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 25%(w/v) Jeffamine ED-2001, 0.1M MES
Crystal Properties Matthews coefficient Solvent content 2.06 39.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.521 α = 90 b = 57.808 β = 90 c = 74.963 γ = 90
Symmetry Space Group P 21 21 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 RAYONIX MX300HE 2016-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.900 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.198 50 97.2 0.082 0.088 0.033 22.1 7.4 69599
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.198 1.22 95.1 0.976 0.056 0.022 0.7 2.2 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 5WSD 1.198 30 64182 3387 92.2 0.1508 0.1508 0.1378 0.1857 0.1664 RANDOM 22.0188
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]
RMS Deviations Key Refinement Restraint Deviation s_non_zero_chiral_vol 0.703 s_from_restr_planes 0.419 s_approx_iso_adps 0.133 s_zero_chiral_vol 0.065 s_similar_adp_cmpnt 0.045 s_rigid_bond_adp_cmpnt 0.026 s_angle_d 0.023 s_bond_d 0.007 s_similar_dist s_anti_bump_dis_restr
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1836 Nucleic Acid Atoms Solvent Atoms 278 Heterogen Atoms 2
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling PHASER phasing SHELX refinement PDB_EXTRACT data extraction