☰ Navigation Tabs
Crystal Structure of the Reassembled Venus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MYW PDB ENTRY 1MYW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 25% PEG 3350, 0.1M HEPES, 0.2M lithium sulfate , pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.2 44.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.054 α = 90 b = 116.046 β = 90 c = 156.852 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 ADSC QUANTUM 315r 2010-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.00 Photon Factory BL-5A
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 2.1 50 94.7 0.102 23.9 11 63893 60532
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 2.1 2.18 99.9 0.329 5.8 9.3
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 THROUGHOUT PDB ENTRY 1MYW 2.1 49.9 60532 3231 99.9 0.17007 0.16693 0.167 0.22919 0.2276 RANDOM 17.411
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] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.421 r_dihedral_angle_3_deg 17.044 r_dihedral_angle_4_deg 15.633 r_dihedral_angle_1_deg 7.124 r_scangle_it 4.277 r_scbond_it 2.669 r_angle_refined_deg 1.78 r_mcangle_it 1.685 r_mcbond_it 0.9 r_chiral_restr 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.421 r_dihedral_angle_3_deg 17.044 r_dihedral_angle_4_deg 15.633 r_dihedral_angle_1_deg 7.124 r_scangle_it 4.277 r_scbond_it 2.669 r_angle_refined_deg 1.78 r_mcangle_it 1.685 r_mcbond_it 0.9 r_chiral_restr 0.11 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7185 Nucleic Acid Atoms Solvent Atoms 651 Heterogen Atoms 30
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling