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Crystal structure of tudor domain 1 of human PHD finger protein 20
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2RHU pdb entries 2rhu, 2eqm experimental model PDB 2EQM pdb entries 2rhu, 2eqm
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 291 25% PEG-3350, 0.2M ammonium acetate, 0.1M bis-tris. Prior to freezing, a cluster of thin rods was transferred to a drop of paratone oil. A fragment of the cluster was frozen in a stream of cold nitrogen., pH 5.5, vapor diffusion, sitting drop, temperature 291K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.03 39.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.498 α = 90 b = 41.062 β = 110.33 c = 28.632 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 IMAGE PLATE RIGAKU RAXIS 2010-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E 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 2.35 20 99.8 0.1 9.1 3.4 2828
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 2.35 2.43 100 0.654 3.3 288
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 entries 2rhu, 2eqm 2.35 19.08 2804 131 0.2074 0.205 0.2123 0.2601 0.2665 RANDOM 43.4265
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] -10.0894 -14.2796 8.2424 1.847
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.94 t_omega_torsion 3.27 t_angle_deg 1.04 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.94 t_omega_torsion 3.27 t_angle_deg 1.04 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 549 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms 1
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing BUSTER-TNT refinement PDB_EXTRACT data extraction StructureStudio data collection HKL-2000 data reduction HKL-2000 data scaling BUSTER refinement