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Crystal structure of Predicted metal-dependent phosphoesterase (PHP family) (tm0559) from THERMOTOGA MARITIMA at 2.40 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 6.5 277 0.1M KH2PO4, 2.0M NaCl, 0.1M NaH2PO4, 0.1M MES , pH 6.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.92 57.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.307 α = 90 b = 111.307 β = 90 c = 383.222 γ = 120
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 315 flat mirror 2005-04-08 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD MARMOSAIC 325 mm CCD 2005-03-31 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.953690 SSRL BL11-1 2 SYNCHROTRON SSRL BEAMLINE BL9-2 0.89194, 0.97944 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.26 29.1 99.5 0.13 0.13 4.5 3.4 83429
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1,2 2.26 2.32 99.4 0.707 0.707 1 2.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2.4 29 65772 3516 99.99 0.172 0.169 0.1804 0.22 0.1963 RANDOM 30.366
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] -1.23 -0.61 -1.23 1.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.934 r_dihedral_angle_4_deg 18.129 r_dihedral_angle_3_deg 16.499 r_dihedral_angle_1_deg 7.168 r_scangle_it 5.222 r_scbond_it 3.947 r_mcangle_it 2.18 r_mcbond_it 1.863 r_angle_refined_deg 1.349 r_angle_other_deg 0.771
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.934 r_dihedral_angle_4_deg 18.129 r_dihedral_angle_3_deg 16.499 r_dihedral_angle_1_deg 7.168 r_scangle_it 5.222 r_scbond_it 3.947 r_mcangle_it 2.18 r_mcbond_it 1.863 r_angle_refined_deg 1.349 r_angle_other_deg 0.771 r_mcbond_other 0.557 r_symmetry_vdw_other 0.22 r_nbd_refined 0.201 r_nbtor_refined 0.18 r_nbd_other 0.175 r_symmetry_hbond_refined 0.142 r_xyhbond_nbd_refined 0.139 r_symmetry_vdw_refined 0.129 r_nbtor_other 0.086 r_chiral_restr 0.076 r_metal_ion_refined 0.046 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10920 Nucleic Acid Atoms Solvent Atoms 212 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling SHELXE model building