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Crystal structure analysis of Dim2p from Pyrococcus horikoshii OT3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TUA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.2 293 9% PEG 3000, 0.1M cacodylate buffer, 0.2M Magnesium Chloride, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.08 40.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.949 α = 90 b = 47.45 β = 90 c = 95.722 γ = 90
Symmetry Space Group P 21 21 21
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 2005-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0000 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2 50 14199 34.7
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 1TUA 2.3 47.84 9135 467 98.18 0.22926 0.22756 0.2218 0.26258 0.2206 RANDOM 25.972
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] 2.26 1.33 -3.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.636 r_dihedral_angle_4_deg 18.369 r_dihedral_angle_3_deg 17.835 r_dihedral_angle_1_deg 5.997 r_scangle_it 3.574 r_scbond_it 2.223 r_angle_refined_deg 1.466 r_mcangle_it 1.374 r_mcbond_it 0.839 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.636 r_dihedral_angle_4_deg 18.369 r_dihedral_angle_3_deg 17.835 r_dihedral_angle_1_deg 5.997 r_scangle_it 3.574 r_scbond_it 2.223 r_angle_refined_deg 1.466 r_mcangle_it 1.374 r_mcbond_it 0.839 r_nbtor_refined 0.301 r_nbd_refined 0.213 r_symmetry_hbond_refined 0.208 r_symmetry_vdw_refined 0.177 r_xyhbond_nbd_refined 0.144 r_chiral_restr 0.099 r_bond_refined_d 0.016 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1320 Nucleic Acid Atoms Solvent Atoms 20 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing