4P14 | pdb_00004p14

Crystal structure of Canavalia brasiliensis (ConBr) complexed with adenine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4H55 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2981.8 M ammonium sulfate, 0.2 M sodium chloride, 0.1 M HEPES, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.2745.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.12α = 90
b = 70.94β = 90
c = 97.43γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 130 mm2008-07-25SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS BEAMLINE D03B-MX11.430LNLSD03B-MX1

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
1222.56990.06718.69.515266
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)
122.051000.364.89.4

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4H55222.31526680699.890.178050.175490.190.227970.23RANDOM35.118
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]
0.06-0.080.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.65
r_dihedral_angle_4_deg20.465
r_sphericity_free18.132
r_dihedral_angle_3_deg14.18
r_sphericity_bonded8.476
r_dihedral_angle_1_deg8.125
r_rigid_bond_restr5.776
r_scangle_other4.435
r_long_range_B_refined4.269
r_long_range_B_other4.258
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.65
r_dihedral_angle_4_deg20.465
r_sphericity_free18.132
r_dihedral_angle_3_deg14.18
r_sphericity_bonded8.476
r_dihedral_angle_1_deg8.125
r_rigid_bond_restr5.776
r_scangle_other4.435
r_long_range_B_refined4.269
r_long_range_B_other4.258
r_scbond_it4.256
r_scbond_other4.243
r_mcbond_it3.95
r_mcbond_other3.947
r_mcangle_it3.892
r_mcangle_other3.891
r_angle_refined_deg2.001
r_angle_other_deg0.887
r_chiral_restr0.111
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d0.003
r_gen_planes_other0.002
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_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1795
Nucleic Acid Atoms
Solvent Atoms84
Heterogen Atoms39

Software

Software
Software NamePurpose
REFMACrefinement