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The crystal structure of Ebp1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WKM 1WKM.pdb
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 298 2.3 M Ammoniumsulfate, 0.1M Citric acid, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.8 56.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.887 α = 90 b = 73.887 β = 90 c = 183.348 γ = 90
Symmetry Space Group P 41 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 100 CCD ADSC QUANTUM 315 MIRROR 2006-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.980 ESRF ID23-1
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 1.6 68 99.8 0.061 12.9 3.8 67896
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) 1 1.6 1.69 100 0.407 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 1WKM.pdb 1.6 57.54 64263 3451 99.73 0.18416 0.18235 0.1802 0.21852 0.2168 RANDOM 22.752
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] 0.38 0.38 -0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.638 r_dihedral_angle_4_deg 16.707 r_dihedral_angle_3_deg 13.139 r_dihedral_angle_1_deg 5.639 r_sphericity_free 4.331 r_sphericity_bonded 4.251 r_scangle_it 3.752 r_scbond_it 2.956 r_rigid_bond_restr 2.481 r_mcangle_it 1.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.638 r_dihedral_angle_4_deg 16.707 r_dihedral_angle_3_deg 13.139 r_dihedral_angle_1_deg 5.639 r_sphericity_free 4.331 r_sphericity_bonded 4.251 r_scangle_it 3.752 r_scbond_it 2.956 r_rigid_bond_restr 2.481 r_mcangle_it 1.75 r_angle_refined_deg 1.229 r_mcbond_it 1.203 r_nbtor_refined 0.3 r_symmetry_vdw_refined 0.213 r_nbd_refined 0.195 r_xyhbond_nbd_refined 0.125 r_symmetry_hbond_refined 0.124 r_chiral_restr 0.09 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2764 Nucleic Acid Atoms Solvent Atoms 487 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling PHASER phasing