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Crystal structure of prApe1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JGF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 50% (v/v) PEG 200, 200 mM Magnesium chloride, 100 mM sodium cacodylate
Crystal Properties Matthews coefficient Solvent content 2.89 57.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.428 α = 90 b = 140.428 β = 90 c = 348.922 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 210 2006-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
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 2.1 500 100 0.045 20.3 5.4 123984
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 2.18 100 0.19 5.4 5
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 5JGF 2.1 44.79 123984 13720 91.85 0.18332 0.18065 0.1867 0.20737 0.2128 RANDOM 36.387
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] 1.66 0.83 1.66 -5.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.136 r_dihedral_angle_4_deg 13.916 r_dihedral_angle_3_deg 12.094 r_dihedral_angle_1_deg 6.021 r_long_range_B_refined 5.584 r_long_range_B_other 5.559 r_angle_refined_deg 1.208 r_angle_other_deg 0.892 r_mcangle_it 0.748 r_mcangle_other 0.748
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.136 r_dihedral_angle_4_deg 13.916 r_dihedral_angle_3_deg 12.094 r_dihedral_angle_1_deg 6.021 r_long_range_B_refined 5.584 r_long_range_B_other 5.559 r_angle_refined_deg 1.208 r_angle_other_deg 0.892 r_mcangle_it 0.748 r_mcangle_other 0.748 r_scangle_other 0.415 r_mcbond_it 0.397 r_mcbond_other 0.397 r_scbond_it 0.351 r_scbond_other 0.351 r_chiral_restr 0.071 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14619 Nucleic Acid Atoms Solvent Atoms 819 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing