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Crystal structure of a C-terminally truncated trimeric ectodomain of the Arabidopsis thaliana gamete fusion protein HAP2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MF1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 293 100 mM Sodium Citrate pH 4.5
200 mM zinc acetate
Crystal Properties Matthews coefficient Solvent content 3.27 62.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.255 α = 90 b = 77.255 β = 90 c = 219.526 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 110 CCD ADSC QUANTUM 315r 2016-05-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97950 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.75 50 56.1 0.995 7.83 3.5 21328 63.42
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.75 2.82 16.7 0.325 1.25 3.3
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 5MF1 2.75 42.43 10646 520 55.36 0.2332 0.231 0.2447 0.2774 0.302 RANDOM 67.8
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] -4.6453 -4.6453 9.2905
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.78 t_omega_torsion 1.68 t_angle_deg 0.91 t_bond_d 0.007 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.78 t_omega_torsion 1.68 t_angle_deg 0.91 t_bond_d 0.007 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3511 Nucleic Acid Atoms Solvent Atoms 43 Heterogen Atoms 65
Software Software Software Name Purpose BUSTER refinement XDS data reduction XSCALE data scaling STARANISO data scaling PHASER phasing