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Crystal structure of YPT32 in complex with GDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CPJ PDB ENTRY 3CPJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 PEG 4000, MGCL2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.45 49.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130 α = 90 b = 45.2 β = 110.5 c = 73.4 γ = 90
Symmetry Space Group C 1 2 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 225 mm CCD 2009-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 ESRF BM14
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 1.7 68.75 99.4 0.052 44104 -3 24.66
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 1.7 1.75 98.9 0.401 3.9
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 PDB ENTRY 3CPJ 1.7 68.75 44104 2223 99.5 0.169 0.167 0.1825 0.203 0.22 RANDOM 20.173
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] -0.37 -0.08 0.15 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.159 r_dihedral_angle_4_deg 18.007 r_dihedral_angle_3_deg 14.316 r_dihedral_angle_1_deg 5.753 r_scangle_it 3.029 r_scbond_it 1.944 r_mcangle_it 1.418 r_angle_refined_deg 1.333 r_mcbond_it 0.778 r_chiral_restr 0.109
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.159 r_dihedral_angle_4_deg 18.007 r_dihedral_angle_3_deg 14.316 r_dihedral_angle_1_deg 5.753 r_scangle_it 3.029 r_scbond_it 1.944 r_mcangle_it 1.418 r_angle_refined_deg 1.333 r_mcbond_it 0.778 r_chiral_restr 0.109 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2700 Nucleic Acid Atoms Solvent Atoms 495 Heterogen Atoms 58
Software Software Software Name Purpose MxCuBE data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling