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Crystal structure of yeast primase catalytic subunit
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MHQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.5 298 0.1M Na-Citrate, 0.2M NDSB, 5mM CdCl2, 30% PEG 600, 10mM ZnCl2 , pH 5.5, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.41 49.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.37 α = 90 b = 196.04 β = 114.72 c = 53.96 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 95 CCD ADSC QUANTUM 210r M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.2826 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 1.6 50 92.6 0.108 10.17 5.6 111075 111075
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 1.6 1.64 59.8 1.988 0.89 3.6 5296
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 (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 4MHQ 1.6 43.88 111075 105430 5568 92.81 0.25689 0.25496 0.268 0.29293 0.2979 RANDOM 28.749
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] -0.31 0.23 -0.54 0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.871 r_dihedral_angle_4_deg 17.112 r_dihedral_angle_3_deg 16.754 r_dihedral_angle_1_deg 7.129 r_angle_refined_deg 1.545 r_angle_other_deg 1.151 r_chiral_restr 0.092 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.871 r_dihedral_angle_4_deg 17.112 r_dihedral_angle_3_deg 16.754 r_dihedral_angle_1_deg 7.129 r_angle_refined_deg 1.545 r_angle_other_deg 1.151 r_chiral_restr 0.092 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.004 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6510 Nucleic Acid Atoms Solvent Atoms 395 Heterogen Atoms 36
Software Software Software Name Purpose XDS data scaling PHASER phasing REFMAC refinement XDS data reduction