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New Crystal Structure of Chlorella Virus DNA Ligase-Adenylate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FVI PDB ENTRY 1FVI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 hanging drops 7.5 277 4-6% PEG 4000, 50 mM HEPES, 50 mM sodium acetate, pH 7.5, hanging drops, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.76 55.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.059 α = 90 b = 60.574 β = 90 c = 70.268 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV 2002-01-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.5418
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 2.95 15 96.9 0.092 3.5 8265 8265 26.2
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 1FVI 2.95 15 8265 7585 680 96.86 0.26641 0.26299 0.2506 0.30351 0.3016 RANDOM 26.237
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] 4.92 0.37 -5.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.004 r_dihedral_angle_3_deg 23.032 r_dihedral_angle_4_deg 14.84 r_dihedral_angle_1_deg 7.828 r_scangle_it 1.924 r_angle_refined_deg 1.575 r_scbond_it 1.153 r_mcangle_it 0.777 r_mcbond_it 0.414 r_symmetry_vdw_refined 0.289
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.004 r_dihedral_angle_3_deg 23.032 r_dihedral_angle_4_deg 14.84 r_dihedral_angle_1_deg 7.828 r_scangle_it 1.924 r_angle_refined_deg 1.575 r_scbond_it 1.153 r_mcangle_it 0.777 r_mcbond_it 0.414 r_symmetry_vdw_refined 0.289 r_nbd_refined 0.251 r_xyhbond_nbd_refined 0.213 r_symmetry_hbond_refined 0.202 r_chiral_restr 0.128 r_bond_refined_d 0.013 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2228 Nucleic Acid Atoms Solvent Atoms 2 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement CrystalClear data reduction SCALEPACK data scaling AMoRE phasing