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Crystal structure of VC2308 protein
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 Tacsimate 35%, Phenol 10mM, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.9 35.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.387 α = 90 b = 64.683 β = 90 c = 81.592 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 MX-225 beryllium lenses 2010-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.979 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.16 50 97.8 0.094 0.094 23.8 9.12 115862 115862 -3 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.16 1.18 84.5 0.61 0.61 1.9 5.7 4962
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.16 50 109812 109812 5797 97.77 0.1448 0.1448 0.14357 0.1398 0.16775 0.1624 RANDOM 8.231
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] -0.24 -0.25 0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.697 r_dihedral_angle_4_deg 13.788 r_dihedral_angle_3_deg 12.98 r_dihedral_angle_1_deg 6.053 r_scangle_it 4.236 r_scbond_it 2.926 r_angle_other_deg 2.334 r_mcangle_it 1.932 r_mcbond_other 1.543 r_angle_refined_deg 1.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.697 r_dihedral_angle_4_deg 13.788 r_dihedral_angle_3_deg 12.98 r_dihedral_angle_1_deg 6.053 r_scangle_it 4.236 r_scbond_it 2.926 r_angle_other_deg 2.334 r_mcangle_it 1.932 r_mcbond_other 1.543 r_angle_refined_deg 1.5 r_rigid_bond_restr 1.373 r_mcbond_it 1.297 r_chiral_restr 0.091 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_gen_planes_other 0.005 r_bond_other_d 0.002 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2927 Nucleic Acid Atoms Solvent Atoms 579 Heterogen Atoms 3
Software Software Software Name Purpose MD2 data collection HKL-3000 phasing DM model building SHELXD phasing SHELXE model building ARP/wARP model building CCP4 model building REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling DM phasing CCP4 phasing