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Crystal structure of Chlorella virus vAL-1 soaked in 200mM D-glucuronic acid, 10% PEG-3350, and 200mM glycine-NaOH (pH 10.0)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GNE PDB ENTRY 3GNE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 12% PEG 3350, 0.2M ammonium formate, 0.1M hepes-NaOH pH7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.58 52.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.402 α = 90 b = 71.121 β = 90 c = 100.705 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 RIGAKU JUPITER 210 2009-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1 SPring-8 BL38B1
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 1.66 26.32 97.5 0.04 74.6 5.4 34464 34464
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 1.66 1.72 97.5 0.144 16.5 5.1 3330
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 (All) 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 AB INITIO FREE R PDB ENTRY 3GNE 1.66 10 32576 32576 1711 93 0.1634 0.1634 0.1606 0.1522 0.2163 0.1605 RANDOM
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 14 2363.52
RMS Deviations Key Refinement Restraint Deviation s_non_zero_chiral_vol 0.061 s_similar_adp_cmpnt 0.059 s_zero_chiral_vol 0.05 s_from_restr_planes 0.0302 s_angle_d 0.025 s_bond_d 0.009 s_anti_bump_dis_restr 0.009 s_similar_dist s_rigid_bond_adp_cmpnt s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1901 Nucleic Acid Atoms Solvent Atoms 453 Heterogen Atoms 12
Software Software Software Name Purpose HKL-2000 data collection CNS refinement SHELXL-97 refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing