X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 5.8
Temperature 290.0
Details potassium phosphate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 290K, pH 5.80

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 33.26 α = 90
b = 45.46 β = 96.12
c = 65.02 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2001-04-25
Diffraction Radiation
Monochromator Protocol
CRYSTAL 3 WAVELENGTH MA
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 0.97965, 0.97979, 0.96863 ESRF ID14-4

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
1.4 25 93.0 0.042 0.033 -- 5.1 -- 43111 -- 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)
1.39 1.43 87.8 0.11 0.09 3.0 4.2 --

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 1.4 12.0 -- 0.0 -- 40455 2195 79.83 -- 0.16126 0.16013 0.18187 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 1.25 1.282 -- 46 792 0.212 0.275 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 9.15
Anisotropic B[1][1] 0.33
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.09
Anisotropic B[2][2] -0.06
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.29
RMS Deviations
Key Refinement Restraint Deviation
p_scangle_it 2.757
p_scbond_it 1.805
p_bond_d 0.009
p_angle_d 1.336
p_planar_d 0.004
p_hb_or_metal_coord 0.202
p_plane_restr 0.004
p_chiral_restr 0.071
p_singtor_nbd 4.276
p_multtor_nbd 18.436
p_xyhbond_nbd 0.308
p_xhyhbond_nbd 0.111
p_mcbond_it 0.793
p_mcangle_it 1.341
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1571
Nucleic Acid Atoms 0
Heterogen Atoms 5
Solvent Atoms 433

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CCP4, OTHER Structure Solution
REFMAC Structure Refinement
Software
Software Name Purpose
REFMAC version: 5 refinement
OTHER model building
CCP4 model building
SCALEPACK data reduction
DENZO data collection