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Crystal structure of the H2Db in complex with the NP-N3D peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HUU PDB ENTRY 4HUU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 0.1 M Tris-HCl, pH 8.5, 0.2 M lithium sulfate, 25-30% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.67 53.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.567 α = 90 b = 85.464 β = 90.18 c = 138.506 γ = 90
Symmetry Space Group P 1 21 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 315r 2012-04-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.956 Australian Synchrotron MX2
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 2.8 138.505 99.9 0.096 3.8 47116 47116 76.45
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.95 100 0.604 0.604 2.3 3.8
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 PDB ENTRY 4HUU 2.8 59.01 47090 2382 99.79 0.1894 0.1858 0.1969 0.2584 0.277 RANDOM 54.4254
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] 3.8651 2.2939 6.2787 -10.1438
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 23.11 t_omega_torsion 2.88 t_angle_deg 1.19 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 23.11 t_omega_torsion 2.88 t_angle_deg 1.19 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 12517 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms 25
Software Software Software Name Purpose SCALA data scaling PHASER phasing BUSTER-TNT refinement PDB_EXTRACT data extraction Blu-Ice data collection XSCALE data scaling BUSTER refinement