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X-ray structure of protein from Arabidopsis thaliana AT1G79260 with Bound Heme
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2A13 PDB entry 2A13
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 Protein Solution (16.5 mg/mL native protein [Heme was added in purification step],
0.050 M sodium chloride, 0.0003 M TCEP, 0.005 M MES pH 6.0)
mixed in a 1:1 ratio with the Well Solution
(24% PEG 4K, 0.05 M BTP pH 7.0 )
Cryoprotected with 30% PEG 4K, 0.05 M BTP pH 7.0 and 15% ethylene glycol, vapor diffusion, hanging drop, temperature 277K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.4 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.749 α = 90 b = 79.732 β = 90 c = 36.971 γ = 90
Symmetry Space Group P 21 21 2
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 MARMOSAIC 300 mm CCD Beryllium lenses 2008-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 1.358 50 97.2 0.041 22.969 4.7 37822
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) 1.36 1.41 97.6 0.236 5.074 3.7 3728
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 2A13 1.358 47.836 37799 1864 97.155 0.171 0.17 0.2144 0.198 0.2385 RANDOM 15.287
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] 0.657 -0.694 0.037
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.402 r_dihedral_angle_4_deg 22.207 r_dihedral_angle_3_deg 11.129 r_dihedral_angle_1_deg 6.236 r_scangle_it 2.512 r_scbond_it 1.759 r_angle_refined_deg 1.354 r_mcangle_it 1.246 r_mcbond_it 0.769 r_nbtor_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.402 r_dihedral_angle_4_deg 22.207 r_dihedral_angle_3_deg 11.129 r_dihedral_angle_1_deg 6.236 r_scangle_it 2.512 r_scbond_it 1.759 r_angle_refined_deg 1.354 r_mcangle_it 1.246 r_mcbond_it 0.769 r_nbtor_refined 0.297 r_nbd_refined 0.205 r_symmetry_vdw_refined 0.17 r_symmetry_hbond_refined 0.119 r_xyhbond_nbd_refined 0.118 r_chiral_restr 0.089 r_bond_refined_d 0.01 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1236 Nucleic Acid Atoms Solvent Atoms 253 Heterogen Atoms 47
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction