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GMPPCP complex of SRP GTPase Ffh NG Domain at ultra-high resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JPN PDB ENTRY 1JPN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.7 30% MPD, 0.1M NAACETATE, PH4.7, 20MM CACL2, 0.15M KOACETATE, 2MM MGCL2, 2MM GMPPCP
Crystal Properties Matthews coefficient Solvent content 2.51 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.006 α = 90 b = 54.44 β = 97.16 c = 98.831 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 ADSC CCD 2002-04-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 5ID-B APS 5ID-B
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 1.15 19.6 94.3 0.06 29.7 4.5 192311 3
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 1.15 1.18 90.9 0.3 3.4 3
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 1JPN 1.15 19.61 169992 13065 89.8 0.146 0.143 0.144 0.18 0.179 RANDOM 17.59
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] -0.25 -0.44 0.16 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.206 r_dihedral_angle_4_deg 13.878 r_dihedral_angle_3_deg 12.466 r_scangle_it 10.705 r_scbond_it 8.299 r_dihedral_angle_1_deg 5.527 r_mcangle_it 4.739 r_mcbond_it 4.156 r_mcbond_other 1.657 r_angle_refined_deg 1.487
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.206 r_dihedral_angle_4_deg 13.878 r_dihedral_angle_3_deg 12.466 r_scangle_it 10.705 r_scbond_it 8.299 r_dihedral_angle_1_deg 5.527 r_mcangle_it 4.739 r_mcbond_it 4.156 r_mcbond_other 1.657 r_angle_refined_deg 1.487 r_angle_other_deg 0.772 r_symmetry_vdw_refined 0.274 r_symmetry_vdw_other 0.257 r_nbd_refined 0.232 r_symmetry_hbond_refined 0.217 r_xyhbond_nbd_refined 0.21 r_nbd_other 0.176 r_nbtor_refined 0.169 r_xyhbond_nbd_other 0.095 r_nbtor_other 0.082 r_chiral_restr 0.067 r_symmetry_metal_ion_refined 0.035 r_metal_ion_refined 0.011 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.004 r_gen_planes_other 0.002 r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4557 Nucleic Acid Atoms Solvent Atoms 585 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling REFMAC phasing