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Crystal structure of the neutralizing Fab fragment AbD1556 bound to the BMP type I receptor IA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AQK PDB ENTRY 1AQK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 294 100mM Tris-HCl pH 7.0, 20% (w/v) PEG 8000 and 10% (w/v) glucose , VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.34 47.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.32 α = 90 b = 129.255 β = 92.27 c = 100.239 γ = 90
Symmetry Space Group P 1 21 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 IMAGE PLATE RIGAKU RAXIS IV++ Varimax Cu HighRes 2005-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.7 30.4 95.3 0.08 0.08 8.2 2.6 62444 59539 65.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.7 2.8 97.8 0.341 0.341 2.7 2.6 6237
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 1AQK 2.7 30.4 56514 3020 95.26 0.23643 0.23409 0.2348 0.28044 0.2789 RANDOM 64.104
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] 3.25 0.99 -1.23 -1.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.169 r_dihedral_angle_4_deg 22.56 r_dihedral_angle_3_deg 21.787 r_dihedral_angle_1_deg 7.65 r_angle_refined_deg 1.624 r_scangle_it 0.882 r_mcangle_it 0.828 r_scbond_it 0.624 r_mcbond_it 0.533 r_chiral_restr 0.114
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.169 r_dihedral_angle_4_deg 22.56 r_dihedral_angle_3_deg 21.787 r_dihedral_angle_1_deg 7.65 r_angle_refined_deg 1.624 r_scangle_it 0.882 r_mcangle_it 0.828 r_scbond_it 0.624 r_mcbond_it 0.533 r_chiral_restr 0.114 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 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 15323 Nucleic Acid Atoms Solvent Atoms 27 Heterogen Atoms
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement CrystalClear data reduction CrystalClear data scaling