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Crystal Structure HP-NAP from strain YS29 cadmium loaded (Cocrystallization 50mM)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TA8 PDB ENTRY 3TA8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 50mM cadmium sulfate, 1.0M sodium acetate, 0.1M HEPES-NaOH, 0.1M L-Arginine, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.59 65.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 187.412 α = 90 b = 187.412 β = 90 c = 187.412 γ = 90
Symmetry Space Group F 4 3 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 4r mirrors 2007-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A 0.9780 Photon Factory BL-6A
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 2.2 20 99.4 0.08 38.1 10.4 14790 26.2
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 2.2 2.28 99.6 0.383 8.2
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 3TA8 2.2 19.65 14722 1486 99.31 0.2155 0.213 0.237 0.2057 RANDOM 24.2293
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.732 r_dihedral_angle_4_deg 18.22 r_dihedral_angle_3_deg 15.738 r_dihedral_angle_1_deg 4.684 r_scangle_it 1.964 r_scbond_it 1.111 r_angle_refined_deg 0.961 r_mcangle_it 0.685 r_mcbond_it 0.325 r_chiral_restr 0.071
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.732 r_dihedral_angle_4_deg 18.22 r_dihedral_angle_3_deg 15.738 r_dihedral_angle_1_deg 4.684 r_scangle_it 1.964 r_scbond_it 1.111 r_angle_refined_deg 0.961 r_mcangle_it 0.685 r_mcbond_it 0.325 r_chiral_restr 0.071 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1186 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing