6L2F

Crystal structure of a cupin protein (tm1459, H54AH58A mutant) in copper (Cu) substituted form


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP629325%(w/v) Jeffamine ED-2001, 0.1M MES
Crystal Properties
Matthews coefficientSolvent content
2.0539.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.635α = 90
b = 57.797β = 90
c = 74.402γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2016-09-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.900SPring-8BL44XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.23501000.0760.0810.0329.47.263984
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.231.2599.90.9710.0320.0120.9993.277.1

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 DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5WSD1.23306071032021000.1460.1460.1881RANDOM18.9856
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]
RMS Deviations
KeyRefinement Restraint Deviation
s_non_zero_chiral_vol0.709
s_from_restr_planes0.394
s_approx_iso_adps0.127
s_zero_chiral_vol0.061
s_similar_adp_cmpnt0.046
s_rigid_bond_adp_cmpnt0.027
s_angle_d0.023
s_bond_d0.007
s_similar_dist
s_anti_bump_dis_restr
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1827
Nucleic Acid Atoms
Solvent Atoms226
Heterogen Atoms38

Software

Software
Software NamePurpose
HKL-2000data scaling
SHELXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing