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Crystal Structure of a novel disintegrin from Saw-scaled viper at 3.2 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RMR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 298 1.2M AMMONIUM SULFATE, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 4 70
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.368 α = 90 b = 91.368 β = 90 c = 54.941 γ = 90
Symmetry Space Group I 41 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 IMAGE PLATE MARRESEARCH MIRROR 2005-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 3.2 64.55 99.6 0.2 8.3 10 2062 2058 55.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 3.2 3.32 97.6 0.544 3.9 191
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1rmr 3.2 64 2058 1967 91 99.13 0.236 0.23594 0.23432 0.2648 RANDOM 50.852
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] 0.79 0.79 -1.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 23.149 r_scangle_it 7.273 r_scbond_it 4.07 r_dihedral_angle_1_deg 3.343 r_mcangle_it 3.116 r_angle_refined_deg 2.35 r_mcbond_it 1.652 r_angle_other_deg 1.414 r_symmetry_vdw_refined 0.538 r_symmetry_vdw_other 0.419
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 23.149 r_scangle_it 7.273 r_scbond_it 4.07 r_dihedral_angle_1_deg 3.343 r_mcangle_it 3.116 r_angle_refined_deg 2.35 r_mcbond_it 1.652 r_angle_other_deg 1.414 r_symmetry_vdw_refined 0.538 r_symmetry_vdw_other 0.419 r_nbd_other 0.284 r_nbd_refined 0.276 r_chiral_restr 0.137 r_xyhbond_nbd_refined 0.132 r_xyhbond_nbd_other 0.038 r_bond_refined_d 0.024 r_gen_planes_refined 0.016 r_gen_planes_other 0.006 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 490 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing