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Crystal structure of gp41 derived protein complexed with fab 8066
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CMR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 1.2M dibasic Ammonium phosphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.36 47.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.527 α = 90 b = 124.698 β = 90 c = 133.657 γ = 90
Symmetry Space Group P 21 21 21
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 marccd 300 mirror 2009-04-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.05 30 99.2 0.099 15.24 4.8 44497 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.05 2.12 96.6 0.662 1.92 3.5
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 2CMR 2.05 29.45 44497 43032 1414 98.56 0.1943 0.19257 0.1985 0.24512 0.2555 RANDOM 32.47
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] -1.62 -2.41 4.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.635 r_dihedral_angle_3_deg 17.062 r_dihedral_angle_4_deg 16.649 r_scangle_it 8.621 r_scbond_it 6.893 r_mcangle_it 6.332 r_dihedral_angle_1_deg 6.06 r_mcbond_it 4.829 r_angle_refined_deg 1.209 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.635 r_dihedral_angle_3_deg 17.062 r_dihedral_angle_4_deg 16.649 r_scangle_it 8.621 r_scbond_it 6.893 r_mcangle_it 6.332 r_dihedral_angle_1_deg 6.06 r_mcbond_it 4.829 r_angle_refined_deg 1.209 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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 4781 Nucleic Acid Atoms Solvent Atoms 442 Heterogen Atoms 2
Software Software Software Name Purpose MAR345 data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling