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APO-CSP1 (COPPER STORAGE PROTEIN 1) FROM METHYLOSINUS TRICHOSPORIUM OB3B
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5AJF PDB ENTRY 5AJF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.1 M BIS-TRIS, PH 6.5, 25% W/V PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.93 36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.885 α = 90 b = 105.918 β = 112.52 c = 48.657 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 PIXEL DECTRIS PILATUS 6M 2012-09-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 Diamond I02
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 1.5 44.95 99.7 0.07 10.9 3.7 60896 2
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 1.5 1.53 99.8 0.5 2.6 3.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 5AJF 1.5 52.96 57772 3089 99.67 0.12535 0.12249 0.17913 0.1799 RANDOM 17.052
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] -0.2 0.99 -0.6 -0.02
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 36.101 r_dihedral_angle_2_deg 29.122 r_dihedral_angle_4_deg 20.673 r_sphericity_bonded 13.963 r_dihedral_angle_3_deg 13.118 r_rigid_bond_restr 5.34 r_scbond_it 4.118 r_dihedral_angle_1_deg 4.034 r_mcangle_it 2.427 r_angle_other_deg 2.126
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 36.101 r_dihedral_angle_2_deg 29.122 r_dihedral_angle_4_deg 20.673 r_sphericity_bonded 13.963 r_dihedral_angle_3_deg 13.118 r_rigid_bond_restr 5.34 r_scbond_it 4.118 r_dihedral_angle_1_deg 4.034 r_mcangle_it 2.427 r_angle_other_deg 2.126 r_mcbond_it 2.116 r_mcbond_other 2.111 r_angle_refined_deg 1.786 r_chiral_restr 0.107 r_bond_refined_d 0.02 r_bond_other_d 0.015 r_gen_planes_refined 0.012 r_gen_planes_other 0.011 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3140 Nucleic Acid Atoms Solvent Atoms 406 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing