3QR1

Crystal Structure of L. pealei PLC21


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7277.15100mM Bis-Tris, 300 mM NaCl, 35% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
Crystal Properties
Matthews coefficientSolvent content
2.5151.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.367α = 90
b = 148.869β = 90
c = 151.572γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMARMOSAIC 225 mm CCDtiled fiber-optic tapers2009-08-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.979APS21-ID-F

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
13.1301000.1465.47.234741-999999-2
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)
13.13.151000.8147.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3.229.97347412983316151000.216080.213810.25776RANDOM62.61
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]
0.04-0.01-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.083
r_dihedral_angle_3_deg16.723
r_dihedral_angle_4_deg12.116
r_dihedral_angle_1_deg6.022
r_angle_refined_deg1.299
r_scangle_it0.851
r_scbond_it0.554
r_mcangle_it0.318
r_mcbond_it0.175
r_chiral_restr0.086
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.083
r_dihedral_angle_3_deg16.723
r_dihedral_angle_4_deg12.116
r_dihedral_angle_1_deg6.022
r_angle_refined_deg1.299
r_scangle_it0.851
r_scbond_it0.554
r_mcangle_it0.318
r_mcbond_it0.175
r_chiral_restr0.086
r_mcbond_other0.062
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_gen_planes_other0.001
r_bond_other_d
r_angle_other_deg
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12486
Nucleic Acid Atoms
Solvent Atoms38
Heterogen Atoms2

Software

Software
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
DENZOdata reduction