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Crystal structure of DNPH1 (RCL) WITH N6-ISOPENTENYL-AMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FYI PDB ENTRY 4FYI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 18% PEG8K, 100 MM NaCaCo, 200 MM ZINC ACETATE, PH 6.5, vapor diffusion, hanging drop, temperature 291K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.146 α = 90 b = 96.568 β = 101.58 c = 79.034 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 CCD ADSC QUANTUM 315r 2010-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.979756 ESRF BM30A
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 2.24 40.97 92.04 0.05 11.1 3.4 21068 1
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 2.24 2.39 65.4 0.107 6.7 2.8
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 4FYI 2.24 38.71 20988 1077 92.04 0.1765 0.1738 0.1732 0.2272 0.2266 RANDOM 15.7391
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] -0.12 0.1 0.14 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.417 r_dihedral_angle_4_deg 18.896 r_dihedral_angle_3_deg 16.12 r_dihedral_angle_1_deg 5.196 r_scangle_it 1.594 r_angle_refined_deg 1.146 r_scbond_it 0.999 r_mcangle_it 0.603 r_mcbond_it 0.315 r_chiral_restr 0.077
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.417 r_dihedral_angle_4_deg 18.896 r_dihedral_angle_3_deg 16.12 r_dihedral_angle_1_deg 5.196 r_scangle_it 1.594 r_angle_refined_deg 1.146 r_scbond_it 0.999 r_mcangle_it 0.603 r_mcbond_it 0.315 r_chiral_restr 0.077 r_bond_refined_d 0.008 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4139 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 112
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction