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Crystal Structure of C. elegans Ap4A Hydrolase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 293 PEG 4000, ammonium acetate, sodium citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.2 43.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.794 α = 90 b = 72.934 β = 90 c = 61.046 γ = 90
Symmetry Space Group C 2 2 21
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 4 2000-07-11 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX9.6 0.87 SRS PX9.6
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.98 18 99.8 53439 9864 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.98 2.05 97.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1.98 20 9389 9389 474 98 0.19715 0.19631 0.2132 RANDOM 14.727
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] 0.59 0.98 -1.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.81 r_dihedral_angle_1_deg 5.248 r_scangle_it 3.416 r_scbond_it 2.248 r_angle_refined_deg 1.627 r_mcangle_it 1.528 r_mcbond_it 0.893 r_angle_other_deg 0.812 r_symmetry_vdw_other 0.432 r_symmetry_vdw_refined 0.343
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.81 r_dihedral_angle_1_deg 5.248 r_scangle_it 3.416 r_scbond_it 2.248 r_angle_refined_deg 1.627 r_mcangle_it 1.528 r_mcbond_it 0.893 r_angle_other_deg 0.812 r_symmetry_vdw_other 0.432 r_symmetry_vdw_refined 0.343 r_nbd_refined 0.247 r_nbd_other 0.217 r_symmetry_hbond_refined 0.216 r_xyhbond_nbd_refined 0.175 r_chiral_restr 0.096 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_xyhbond_nbd_other 0.005 r_gen_planes_other 0.004 r_bond_other_d 0.001 r_nbtor_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1032 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms
Software Software Software Name Purpose MLPHARE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling