3MF8 | pdb_00003mf8

Crystal Structure of Native cis-CaaD


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2FLTPDB ENTRY 2FLT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1hanging drop9298three micro liter of 14 mg/mL cis-CaaD protein sample mixed with three micro liter crystallization solution: 8 M (NH4)2SO4, 0.1 M Bicine buffer (pH 9.0), hanging drop, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.7630.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.987α = 90
b = 58.987β = 90
c = 58.297γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS2005-03-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

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
12.0151.199.80.04651.610.77768
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)
12.012.0899.20.099.8

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2FLT2.0150739835699.880.186250.183840.170.235740.22RANDOM16.183
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]
0.260.130.26-0.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.17
r_dihedral_angle_3_deg17.8
r_dihedral_angle_4_deg17.688
r_rigid_bond_restr5.925
r_dihedral_angle_1_deg5.707
r_scbond_it5.3
r_sphericity_free4.866
r_scangle_it4.508
r_sphericity_bonded2.816
r_mcangle_it1.605
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.17
r_dihedral_angle_3_deg17.8
r_dihedral_angle_4_deg17.688
r_rigid_bond_restr5.925
r_dihedral_angle_1_deg5.707
r_scbond_it5.3
r_sphericity_free4.866
r_scangle_it4.508
r_sphericity_bonded2.816
r_mcangle_it1.605
r_angle_refined_deg1.412
r_mcbond_it0.968
r_symmetry_hbond_refined0.392
r_nbtor_refined0.307
r_nbd_refined0.233
r_xyhbond_nbd_refined0.224
r_symmetry_vdw_refined0.185
r_chiral_restr0.106
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms912
Nucleic Acid Atoms
Solvent Atoms101
Heterogen Atoms5

Software

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