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Crystal Structure of PBANKA_031420
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HX4 PDB entry 3hx4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 20 % PEG 3350, 0.2 M CaCl2, 5 mM AMPPNP, 5 mM CaCL2, 2.5 mM MgCl2, glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.27 45.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.467 α = 90 b = 107.138 β = 108.21 c = 54.303 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 CCD MARMOSAIC 300 mm CCD 2010-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-1
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 53.57 100 0.118 7.2 4.3 30757 30757
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 2.14 99.9 0.916 1.72 4.2
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 PDB entry 3hx4 2.1 50 30757 29135 1545 99.72 0.19723 0.19443 0.2127 0.25025 0.2641 RANDOM 9.752
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] 1.17 0.08 -0.5 -0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.932 r_dihedral_angle_4_deg 16.086 r_dihedral_angle_3_deg 14.494 r_scangle_it 5.204 r_dihedral_angle_1_deg 4.691 r_scbond_it 3.065 r_mcangle_it 2.193 r_angle_refined_deg 1.514 r_angle_other_deg 1.223 r_mcbond_it 1.205
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.932 r_dihedral_angle_4_deg 16.086 r_dihedral_angle_3_deg 14.494 r_scangle_it 5.204 r_dihedral_angle_1_deg 4.691 r_scbond_it 3.065 r_mcangle_it 2.193 r_angle_refined_deg 1.514 r_angle_other_deg 1.223 r_mcbond_it 1.205 r_mcbond_other 0.139 r_chiral_restr 0.102 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3707 Nucleic Acid Atoms Solvent Atoms 222 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PHASER phasing TNT refinement PDB_EXTRACT data extraction HKL-2000 data collection DENZO data reduction