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Crystal structure of DNPH1 (RCL) with 6-CYCLOPENTYL-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 hanging drop 7.6 291 100 MM TRIS, 1.1 AMMONIUM SULPHATE, 20MM MGSO4, PH 7.6, hanging drop, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.87 34.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.728 α = 90 b = 100.644 β = 101.79 c = 79.681 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 2010-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.97950 ESRF ID14-4
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 1.69 32.03 93.88 0.065 5.4 3.9 53250 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 1.69 1.79 75.8 0.115 2.6 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 1.69 27.02 52987 2671 93.88 0.1778 0.176 0.182 0.2125 0.2178 RANDOM 16.691
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] 0.01 0.05 0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.102 r_dihedral_angle_4_deg 18.385 r_dihedral_angle_3_deg 13.512 r_dihedral_angle_1_deg 5.183 r_scangle_it 2.206 r_scbond_it 1.439 r_angle_refined_deg 1.407 r_mcangle_it 0.848 r_angle_other_deg 0.815 r_mcbond_it 0.477
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.102 r_dihedral_angle_4_deg 18.385 r_dihedral_angle_3_deg 13.512 r_dihedral_angle_1_deg 5.183 r_scangle_it 2.206 r_scbond_it 1.439 r_angle_refined_deg 1.407 r_mcangle_it 0.848 r_angle_other_deg 0.815 r_mcbond_it 0.477 r_mcbond_other 0.133 r_chiral_restr 0.111 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4195 Nucleic Acid Atoms Solvent Atoms 497 Heterogen Atoms 122
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction