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Crystal structure of NaASP2 with Zn2+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1U53 PDB ENTRY 1U53
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 100mM imidazole, 40% PEG 400, 10mM ZnCl2 , pH 8.5, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 1.86 33.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.1 α = 90 b = 51.86 β = 113.88 c = 43.58 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 IMAGE PLATE RIGAKU RAXIS HTC 2013-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
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 1.66 31.6 99.8 0.058 13.5 6.4 18323 18302 3 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 1.66 1.69 96.5 1.832 0.8 5.8 874
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 1U53 1.664 31.6 17287 932 99.43 0.19298 0.19085 0.1792 0.23269 0.2174 RANDOM 32.73
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] 14.66 3.04 -5 -9.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.786 r_dihedral_angle_4_deg 19.991 r_dihedral_angle_3_deg 14.998 r_long_range_B_refined 8.422 r_dihedral_angle_1_deg 6.306 r_scbond_it 5.253 r_mcangle_it 4.176 r_mcbond_it 3.03 r_angle_refined_deg 2.013 r_chiral_restr 0.143
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.786 r_dihedral_angle_4_deg 19.991 r_dihedral_angle_3_deg 14.998 r_long_range_B_refined 8.422 r_dihedral_angle_1_deg 6.306 r_scbond_it 5.253 r_mcangle_it 4.176 r_mcbond_it 3.03 r_angle_refined_deg 2.013 r_chiral_restr 0.143 r_bond_refined_d 0.021 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1424 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 1
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling