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Crystal structure analysis of ColE1 ROM mutant F14Y
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ROP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 273 Well solution: 22% MPD, 0.1 M sodium acetate pH 5.5, 0.1 M sodium chloride. Protein solution: protein 2.5 mg/ml, 0.01 M Tris pH 6.5, 0.05 M sodium chloride. Drops: equal volumes of well and protein solutions., VAPOR DIFFUSION, HANGING DROP, temperature 273K
Crystal Properties Matthews coefficient Solvent content 2.47 50.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.26 α = 90 b = 45.647 β = 90 c = 45.581 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 105 IMAGE PLATE RIGAKU RAXIS IV Blue Max-flux confocal 2005-02-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 1.89 20.01 98.6 0.047 16.3 4.94 17596 17351 28.4
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 1.89 1.96 93.1 0.293 3.8 4.69 1707
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 1ROP 1.9 20 16467 872 98.78 0.20625 0.20323 0.204 0.26257 0.2584 RANDOM 30.9
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] -3.06 1.34 1.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.187 r_dihedral_angle_4_deg 21.463 r_dihedral_angle_3_deg 16.5 r_scangle_it 5.172 r_dihedral_angle_1_deg 5.145 r_scbond_it 3.371 r_mcangle_it 1.959 r_angle_refined_deg 1.643 r_mcbond_it 1.226 r_nbtor_refined 0.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.187 r_dihedral_angle_4_deg 21.463 r_dihedral_angle_3_deg 16.5 r_scangle_it 5.172 r_dihedral_angle_1_deg 5.145 r_scbond_it 3.371 r_mcangle_it 1.959 r_angle_refined_deg 1.643 r_mcbond_it 1.226 r_nbtor_refined 0.296 r_symmetry_hbond_refined 0.271 r_nbd_refined 0.207 r_symmetry_vdw_refined 0.204 r_xyhbond_nbd_refined 0.186 r_chiral_restr 0.105 r_bond_refined_d 0.021 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1369 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection d*TREK data reduction d*TREK data scaling PHASER phasing