X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 291.0
Details PEG 8000, Tris-HCl, NaCl. PEG 400 as cryo protectant., pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 51.47 α = 90
b = 80.22 β = 111.06
c = 54.01 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 MARRESEARCH -- 2000-02-21
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID13 0.782 ESRF ID13

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 19.9 93.7 -- 0.084 -- 4.3 324813 75194 0.0 0.0 15.25
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)
1.4 1.44 80.1 -- 0.369 2.3 2.4 4563

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 1.4 19.9 -- 0.0 74439 70727 3712 94.3 0.1376 0.138 0.1358 0.1732 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 1.42 1.46 3651 191 -- 0.15 0.23 -- 87.0
X Ray Diffraction 1.46 1.5 4346 241 -- 0.15 0.19 -- 79.6
X Ray Diffraction 1.5 1.54 4246 219 -- 0.14 0.23 -- 79.0
X Ray Diffraction 1.54 1.59 4056 226 -- 0.13 0.19 -- 78.7
X Ray Diffraction 1.59 1.64 4872 254 -- 0.12 0.17 -- 96.5
X Ray Diffraction 1.64 1.7 4840 256 -- 0.11 0.16 -- 99.5
X Ray Diffraction 1.7 1.77 4697 227 -- 0.1 0.18 -- 99.8
X Ray Diffraction 1.77 1.84 4527 213 -- 0.11 0.16 -- 99.8
X Ray Diffraction 1.84 1.93 4308 228 -- 0.11 0.16 -- 99.9
X Ray Diffraction 1.93 2.03 4162 232 -- 0.11 0.17 -- 100.0
X Ray Diffraction 2.03 2.15 3926 217 -- 0.12 0.18 -- 100.0
X Ray Diffraction 2.15 2.28 3732 202 -- 0.12 0.18 -- 100.0
X Ray Diffraction 2.28 2.45 3510 197 -- 0.12 0.15 -- 100.0
X Ray Diffraction 2.45 2.66 3240 201 -- 0.13 0.18 -- 100.0
X Ray Diffraction 2.66 2.95 3025 141 -- 0.14 0.16 -- 100.0
X Ray Diffraction 2.95 3.33 2747 143 -- 0.15 0.18 -- 100.0
X Ray Diffraction 3.33 3.95 2439 104 -- 0.15 0.15 -- 99.9
X Ray Diffraction 3.95 5.06 2031 106 -- 0.15 0.15 -- 99.1
X Ray Diffraction 5.06 8.77 1558 75 -- 0.17 0.18 -- 97.3
X Ray Diffraction 8.77 19.8 814 39 -- 0.22 0.25 -- 88.6
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Anisotropic
Mean Isotropic B 17.26
Anisotropic B[1][1] -0.36
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.29
Anisotropic B[2][2] -0.42
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.58
RMS Deviations
Key Refinement Restraint Deviation
p_chiral_restr 0.157
p_plane_restr 0.013
p_scangle_it 5.237
p_scbond_it 3.922
p_mcangle_it 3.417
p_mcbond_it 2.502
p_bond_d 0.021
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.2
Luzzati Sigma A (Observed) 0.07
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.21
Luzzati Sigma A (R-Free Set) 0.11
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3164
Nucleic Acid Atoms 0
Heterogen Atoms 34
Solvent Atoms 432

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
REFMAC Structure Refinement
Software
Software Name Purpose
REFMAC refinement
AMORE model building
SCALEPACK data reduction
DENZO data collection