X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 298.0
Details 0.6 M disodium, 1.0 M monopotassium phosphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 99.83 α = 90
b = 99.83 β = 90
c = 150.33 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2001-04-15
Diffraction Radiation
Monochromator Protocol
Double crystal MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 1.04888, 0.91987, 0.91957, 0.88557 SSRL BL9-2

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
2.42 60 96.8 -- 0.054 -- -- 29713 28463 0.0 -3.0 --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
2.42 2.483 99.5 -- -- -- -- --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MAD 2.42 60.05 -- -- -- 27000 1441 95.73 -- 0.24243 0.24078 0.27303 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 2.42 2.483 -- 120 2026 0.287 0.314 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 60.096
Anisotropic B[1][1] 0.96
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.96
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.93
RMS Deviations
Key Refinement Restraint Deviation
r_xyhbond_nbd_other 0.226
r_nbd_other 0.282
r_mcbond_it 1.78
r_angle_other_deg 1.345
r_gen_planes_refined 0.013
r_scangle_it 6.602
r_bond_refined_d 0.035
r_symmetry_hbond_other 0.062
r_bond_other_d 0.002
r_nbd_refined 0.28
r_nbtor_other 0.343
r_angle_refined_deg 3.034
r_mcangle_it 3.227
r_dihedral_angle_3_deg 24.632
r_gen_planes_other 0.003
r_chiral_restr 0.201
r_symmetry_vdw_refined 0.336
r_dihedral_angle_1_deg 6.173
r_symmetry_vdw_other 0.347
r_scbond_it 4.116
r_xyhbond_nbd_refined 0.237
r_symmetry_hbond_refined 0.31
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2485
Nucleic Acid Atoms 0
Heterogen Atoms 28
Solvent Atoms 46

Software

Software
Software Name Purpose
HKL-2000 data collection
TRUNCATE data reduction
MLPHARE phasing
REFMAC refinement version: 5.0
HKL-2000 data reduction
CCP4 data scaling version: (TRUNCATE)