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_mcangle_it 3.417
p_chiral_restr 0.157
p_mcbond_it 2.502
p_bond_d 0.021
p_scangle_it 5.237
p_scbond_it 3.922
p_plane_restr 0.013
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 3238
Nucleic Acid Atoms 0
Heterogen Atoms 34
Solvent Atoms 432

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing
REFMAC refinement