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Crystal Structure of H2Db-NPM6I
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CPL PDB entry 3cpl
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 0.1M Tris HCl, 0.2M LiSO4, 25-30% PEG 8000, pH 8.5, vapor diffusion, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.81 56.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.69 α = 90 b = 72.27 β = 103.29 c = 86.83 γ = 90
Symmetry Space Group P 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 100 CCD ADSC QUANTUM 210 2008-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.956 Australian Synchrotron MX1
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 50 94.4 0.103 11.54 4.4 68232 25.74
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3cpl 2 42.68 68232 3452 99.91 0.1934 0.1914 0.2311 0.2228 RANDOM 29.89
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] -0.6234 -1.0389 -4.222 4.8454
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.92 t_omega_torsion 3.4 t_angle_deg 1.06 t_bond_d 0.009 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.92 t_omega_torsion 3.4 t_angle_deg 1.06 t_bond_d 0.009 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion 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 6335 Nucleic Acid Atoms Solvent Atoms 848 Heterogen Atoms 8
Software Software Software Name Purpose PHASER phasing BUSTER-TNT refinement PDB_EXTRACT data extraction Blu-Ice data collection XDS data reduction BUSTER refinement