2XDQ

Dark Operative Protochlorophyllide Oxidoreductase (ChlN-ChlB)2 Complex


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.1290PROTEIN CONCENTRATION = 10 MG/ML TEMPERATURE = 17 DEGREES C ATMOSPHERE - ANAEROBIC, REDUCING METHOD - HANGING DROP VOLUMES - 3MICROL PROTEIN - 3MICROL RESERVOIR SOLUTION RESERVOIR - 9.5% PEG 6000, 85MM HEPES PH 7.1, CRYOPROTECTANT - 14% MPD, 15% GLYCEROL
Crystal Properties
Matthews coefficientSolvent content
3.3163

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 192.095α = 90
b = 192.095β = 90
c = 132.504γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2007-12-10MMAD
21x-ray100CCDADSC CCDMMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29
2SYNCHROTRONSOLEIL BEAMLINE PROXIMA 10.9790, 0.9795SOLEILPROXIMA 1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.42599.10.08208.354878155.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.491000.473.58.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSIRASTHROUGHOUTNONE2.4103.6552744281798.60.204080.201270.2569RANDOM69.175
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]
2.821.412.82-4.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.555
r_dihedral_angle_4_deg21.022
r_dihedral_angle_3_deg17.666
r_dihedral_angle_1_deg8.336
r_angle_refined_deg2.023
r_scangle_it1.892
r_scbond_it1.133
r_mcangle_it0.834
r_mcbond_it0.448
r_chiral_restr0.116
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.555
r_dihedral_angle_4_deg21.022
r_dihedral_angle_3_deg17.666
r_dihedral_angle_1_deg8.336
r_angle_refined_deg2.023
r_scangle_it1.892
r_scbond_it1.133
r_mcangle_it0.834
r_mcbond_it0.448
r_chiral_restr0.116
r_bond_refined_d0.02
r_gen_planes_refined0.014
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6793
Nucleic Acid Atoms
Solvent Atoms140
Heterogen Atoms23

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXphasing