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Crystal structure HP-NAP from strain YS39 in apo form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JI4 PDB ENTRY 1JI4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.8 293 0.1M L-arginine, 20% ethylene glycol, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.73 67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 189.465 α = 90 b = 189.465 β = 90 c = 189.465 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 mirror 2010-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
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 99.9 0.064 66.4 13.5 15374 38.9
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 2.24 100 0.365 11.2
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1JI4 2.2 19.34 14456 765 99.74 0.22465 0.22333 0.2153 0.24812 0.239 RANDOM 36.041
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 34.415 r_dihedral_angle_3_deg 14.798 r_dihedral_angle_4_deg 12.76 r_dihedral_angle_1_deg 4.198 r_scangle_it 1.58 r_scbond_it 1.005 r_angle_refined_deg 0.865 r_mcangle_it 0.818 r_mcbond_it 0.477 r_nbtor_refined 0.291
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.415 r_dihedral_angle_3_deg 14.798 r_dihedral_angle_4_deg 12.76 r_dihedral_angle_1_deg 4.198 r_scangle_it 1.58 r_scbond_it 1.005 r_angle_refined_deg 0.865 r_mcangle_it 0.818 r_mcbond_it 0.477 r_nbtor_refined 0.291 r_nbd_refined 0.171 r_symmetry_vdw_refined 0.151 r_xyhbond_nbd_refined 0.128 r_symmetry_hbond_refined 0.112 r_chiral_restr 0.065 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1187 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 4
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling