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Crystal structure of Maf domain of human N-acetylserotonin O-methyltransferase-like protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EX2 PDB entry 1EX2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 300 15% PEG 3350, 0.1 M Succinic acid, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 2.47 50.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.802 α = 90 b = 116.983 β = 90 c = 51.471 γ = 90
Symmetry Space Group P 21 21 2
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 V 2007-01-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54000
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 25.07 99.7 0.167 5.9 6.9 35334 35334
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1EX2 2 25.07 33495 33495 1764 99.82 0.20077 0.20077 0.19795 0.1948 0.25309 0.2487 RANDOM 23.982
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] 0.06 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.186 r_dihedral_angle_4_deg 18.525 r_dihedral_angle_3_deg 16.282 r_dihedral_angle_1_deg 6.31 r_scangle_it 3.016 r_scbond_it 1.905 r_angle_refined_deg 1.429 r_mcangle_it 1.356 r_mcbond_it 0.804 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.186 r_dihedral_angle_4_deg 18.525 r_dihedral_angle_3_deg 16.282 r_dihedral_angle_1_deg 6.31 r_scangle_it 3.016 r_scbond_it 1.905 r_angle_refined_deg 1.429 r_mcangle_it 1.356 r_mcbond_it 0.804 r_nbtor_refined 0.298 r_nbd_refined 0.204 r_symmetry_hbond_refined 0.18 r_xyhbond_nbd_refined 0.177 r_symmetry_vdw_refined 0.166 r_chiral_restr 0.095 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 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 3190 Nucleic Acid Atoms Solvent Atoms 333 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing