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Crystal structure of the complex of Ribosome inactivating protein from Momordica Balsamina with disaccharide, N-Acetylglucosamine (beta-1, 4) Mannose at 1.7 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MRW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.7 298 14% PEG 6000, 0.1M Sodium Phosphate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.4 48.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.39 α = 90 b = 130.39 β = 90 c = 39.808 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 77 CCD MARRESEARCH mirror 2012-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97 ESRF BM14
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 1.7 32.6 99.9 0.044 41.3 27773
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 99.9 0.493 2.3
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 (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 3MRW 1.7 32.6 27773 26375 1394 99.88 0.18487 0.18276 0.1926 0.22569 0.2349 RANDOM 35.204
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] -2.19 -1.1 -2.19 3.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.229 r_dihedral_angle_4_deg 16.079 r_dihedral_angle_3_deg 12.109 r_dihedral_angle_1_deg 5.355 r_scangle_it 4.46 r_scbond_it 3.262 r_angle_refined_deg 2.056 r_mcangle_it 2.044 r_mcbond_it 1.388 r_chiral_restr 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.229 r_dihedral_angle_4_deg 16.079 r_dihedral_angle_3_deg 12.109 r_dihedral_angle_1_deg 5.355 r_scangle_it 4.46 r_scbond_it 3.262 r_angle_refined_deg 2.056 r_mcangle_it 2.044 r_mcbond_it 1.388 r_chiral_restr 0.16 r_bond_refined_d 0.03 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 1911 Nucleic Acid Atoms Solvent Atoms 261 Heterogen Atoms 52
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling