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Structure of myelin P2 protein from Equine spinal cord
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PMP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 293 100mM HEPES, 20%w/v PEG 4000, 15%v/v 2-propanol, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.61 52.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.846 α = 90 b = 45.846 β = 90 c = 125.778 γ = 120
Symmetry Space Group P 32 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 QUANTUM 4 2000-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.1 1.0 SRS PX14.1
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 1PMP 2.1 41.89 8255 414 91.51 0.18845 0.18617 0.1994 0.23332 0.2366 RANDOM 43.642
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] 1.67 0.84 1.67 -2.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.281 r_dihedral_angle_4_deg 23.951 r_dihedral_angle_3_deg 16.469 r_dihedral_angle_1_deg 6.74 r_scangle_it 3.429 r_scbond_it 2.364 r_angle_refined_deg 1.855 r_mcangle_it 1.219 r_mcbond_it 1.021 r_angle_other_deg 0.918
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.281 r_dihedral_angle_4_deg 23.951 r_dihedral_angle_3_deg 16.469 r_dihedral_angle_1_deg 6.74 r_scangle_it 3.429 r_scbond_it 2.364 r_angle_refined_deg 1.855 r_mcangle_it 1.219 r_mcbond_it 1.021 r_angle_other_deg 0.918 r_symmetry_hbond_refined 0.288 r_xyhbond_nbd_refined 0.252 r_nbd_refined 0.244 r_mcbond_other 0.217 r_nbd_other 0.198 r_nbtor_refined 0.171 r_chiral_restr 0.102 r_symmetry_vdw_refined 0.092 r_nbtor_other 0.088 r_symmetry_vdw_other 0.084 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1014 Nucleic Acid Atoms Solvent Atoms 102 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing