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Crystal Structure of Uncharacterized Cupredoxin-like Domain Protein Cupredoxin_1 with Copper Bound from Bacillus anthracis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Structure of the same protein (cupredoxin_1) without copper bound
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 289 120 mM magnessium sulfate, 150 mM formate pH 4.0, 38.6 % w/v PEG1000, 10 mM copper chloride, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.29 46.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.275 α = 90 b = 73.594 β = 116.72 c = 40.366 γ = 90
Symmetry Space Group P 1 21 1
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 ADSC QUANTUM 315r mirrors 2012-08-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97935 APS 19-ID
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 1.7 50 99.5 0.107 11.8 3 21670 21670 17.68
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 1.7 1.73 99.9 0.518 2.48 2.9 1093
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 THROUGHOUT Structure of the same protein (cupredoxin_1) without copper bound 1.703 30.43 21620 21620 1108 98.64 0.179 0.179 0.177 0.1785 0.21 0.2103 random 24.6
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 f_dihedral_angle_d 12.165 f_angle_d 1.199 f_chiral_restr 0.088 f_bond_d 0.008 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1440 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 7
Software Software Software Name Purpose SBC-Collect data collection HKL-3000 data collection HKL-3000 phasing MOLREP phasing PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling