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Low resolution 3D structure of C.elegans globin-like protein (GLB-1): P3121 crystal form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WTG PDB ENTRY 2WTG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 3.0 M AMMONIUM SULPHATE, 10% GLYCEROL
Crystal Properties Matthews coefficient Solvent content 3.6 65.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.681 α = 90 b = 77.681 β = 90 c = 145.64 γ = 120
Symmetry Space Group P 31 2 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 CCD ADSC CCD 2007-01-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 ESRF ID14-3
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 2.8 34.3 98.4 0.06 23.3 9 12777 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 2WTG 2.8 34.28 12139 627 97.83 0.27139 0.269 0.2974 0.31948 0.3481 RANDOM 57.848
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] 0.69 0.35 0.69 -1.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.808 r_dihedral_angle_3_deg 17.442 r_dihedral_angle_4_deg 9.2 r_dihedral_angle_1_deg 4.649 r_scangle_it 1.593 r_mcangle_it 1.339 r_scbond_it 1.152 r_angle_refined_deg 0.996 r_mcbond_it 0.736 r_nbtor_refined 0.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.808 r_dihedral_angle_3_deg 17.442 r_dihedral_angle_4_deg 9.2 r_dihedral_angle_1_deg 4.649 r_scangle_it 1.593 r_mcangle_it 1.339 r_scbond_it 1.152 r_angle_refined_deg 0.996 r_mcbond_it 0.736 r_nbtor_refined 0.296 r_nbd_refined 0.194 r_symmetry_vdw_refined 0.162 r_xyhbond_nbd_refined 0.136 r_symmetry_hbond_refined 0.123 r_chiral_restr 0.064 r_bond_refined_d 0.011 r_gen_planes_refined 0.003 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined 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 2588 Nucleic Acid Atoms Solvent Atoms 46 Heterogen Atoms 141
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing