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Crystal Structure HP-NAP from strain YS39 zinc soaked (20mM)
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, HANGING DROP 8.8 293 0.1M L-Arginine, 20% ethylene glycol, 20mM zinc sulfate, pH 8.8, vapor diffusion, hanging drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.5 64.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 185.529 α = 90 b = 185.529 β = 90 c = 185.529 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 210r mirrors 2009-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.2892 Photon Factory AR-NW12A
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 2.5 50 99.2 0.046 63.6 13.4 9990 62.3
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 2.5 2.54 100 0.371 9.4
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 2.5 20 9792 973 98.52 0.2335 0.2274 0.2911 0.2595 RANDOM 50.3665
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 35.456 r_dihedral_angle_3_deg 21.43 r_dihedral_angle_4_deg 11.771 r_dihedral_angle_1_deg 5.08 r_scangle_it 4.071 r_scbond_it 2.334 r_angle_refined_deg 1.471 r_mcangle_it 1.349 r_mcbond_it 0.637 r_chiral_restr 0.103
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.456 r_dihedral_angle_3_deg 21.43 r_dihedral_angle_4_deg 11.771 r_dihedral_angle_1_deg 5.08 r_scangle_it 4.071 r_scbond_it 2.334 r_angle_refined_deg 1.471 r_mcangle_it 1.349 r_mcbond_it 0.637 r_chiral_restr 0.103 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1179 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms 16
Software Software Software Name Purpose SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling