X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 323.0
Details 20-10% PEG 4000, 200 mM potassium fluoride, 25 mM potassium phosphate, 25 mM ammonium sulfate, 2 mM EDTA, 3mM DTE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 323.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 50.33 α = 100.92
b = 71.45 β = 92.05
c = 77.73 γ = 104.47
Symmetry
Space Group P 1

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH mirrors 1999-07-14
IMAGE PLATE MARRESEARCH mirrors 1999-06-26
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Si 111 and 311 single crystals SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID2 0.9903 ESRF ID2
SYNCHROTRON ESRF BEAMLINE BM30A 0.9801 ESRF BM30A

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
1.63 19.79 92.3 0.146 -- -- 4.1 123475 484600 0.0 -- 23.7
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)
1.63 1.67 56.1 0.316 -- 0.8 1.5 --

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
MOLECULAR REPLACEMENT 1.76 19.79 -- -- 101671 101433 8466 99.8 -- -- 0.192 0.223 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 1.76 1.79 5063 417 4487 0.3043 0.3314 0.015 98.9
X Ray Diffraction 1.79 1.82 5047 439 4651 0.2931 0.3055 0.014 99.1
X Ray Diffraction 1.82 1.86 5132 449 4656 0.2684 0.2891 0.013 99.3
X Ray Diffraction 1.86 1.89 5022 439 4612 0.2448 0.2798 0.012 99.3
X Ray Diffraction 1.89 1.94 5140 437 4707 0.2288 0.2623 0.011 99.3
X Ray Diffraction 1.94 1.98 5059 404 4665 0.2171 0.2521 0.011 99.6
X Ray Diffraction 1.98 2.03 5064 445 4609 0.2421 0.2654 0.012 99.3
X Ray Diffraction 2.03 2.09 5076 398 4694 0.2101 0.2386 0.011 99.7
X Ray Diffraction 2.09 2.15 5040 414 4640 0.2 0.2443 0.01 99.5
X Ray Diffraction 2.15 2.22 5120 426 4696 0.1921 0.2238 0.009 99.6
X Ray Diffraction 2.22 2.29 5110 423 4694 0.2002 0.2341 0.01 99.8
X Ray Diffraction 2.29 2.39 5081 409 4678 0.2116 0.2783 0.011 99.8
X Ray Diffraction 2.39 2.49 5076 400 4683 0.2035 0.2501 0.01 99.8
X Ray Diffraction 2.49 2.63 5060 422 4645 0.1915 0.2178 0.009 99.8
X Ray Diffraction 2.63 2.79 5088 417 4673 0.1838 0.2254 0.009 99.9
X Ray Diffraction 2.79 3.01 5057 429 4646 0.1894 0.2262 0.009 99.9
X Ray Diffraction 3.01 3.31 5078 426 4652 0.1785 0.2073 0.009 99.8
X Ray Diffraction 3.31 3.78 5055 446 4632 0.1699 0.1971 0.008 99.4
X Ray Diffraction 3.78 4.75 5045 435 4608 0.1529 0.175 0.007 99.1
X Ray Diffraction 4.75 19.8 5020 391 4639 0.1944 0.221 0.01 98.7
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 35.55
Anisotropic B[1][1] -1.55
Anisotropic B[1][2] 1.41
Anisotropic B[1][3] 0.77
Anisotropic B[2][2] -3.2
Anisotropic B[2][3] -0.23
Anisotropic B[3][3] 4.75
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 7.82
x_scbond_it 4.76
x_mcangle_it 5.02
x_mcbond_it 3.08
x_torsion_impr_deg 0.73
x_torsion_deg 25.6
x_angle_deg 1.3
x_bond_d 0.005
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.2
Luzzati Sigma A (Observed) 0.21
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.24
Luzzati Sigma A (R-Free Set) 0.23
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8499
Nucleic Acid Atoms 0
Heterogen Atoms 10
Solvent Atoms 475

Software

Computing
Computing Package Purpose
MARXDS Data Reduction (intensity integration)
XDS Data Reduction (data scaling)
AMORE Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
Crystallography & NMR System version: 1.0 refinement