X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 290.0
Details 30 mM ammonium sulfate, 30 mM 40% PEG 4K, 0.1 M Tris pH 8.5, 20 mM 2-ME, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 95.69 α = 90
b = 95.69 β = 90
c = 82.5 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2004-03-20
Diffraction Radiation
Monochromator Protocol
two passes, half degree SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-BM -- APS 22-BM

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
2.7 50 100.0 0.109 -- -- 18.2 -- 12337 -- -- --
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)
2.7 2.8 100.0 0.334 -- -- 17.3 1226

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 2.7 41.44 -- 0.0 -- 12144 1253 98.4 -- -- 0.216 0.259 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 2.7 2.74 443 35 408 0.282 0.373 -- --
X Ray Diffraction 2.74 2.78 464 45 419 0.301 0.388 -- --
X Ray Diffraction 2.78 2.82 474 43 431 0.267 0.392 -- --
X Ray Diffraction 2.82 2.86 461 49 412 0.288 0.336 -- --
X Ray Diffraction 2.86 2.91 468 47 421 0.278 0.358 -- --
X Ray Diffraction 2.91 2.96 471 50 421 0.245 0.265 -- --
X Ray Diffraction 2.96 3.01 482 44 438 0.254 0.38 -- --
X Ray Diffraction 3.01 3.07 474 48 426 0.269 0.315 -- --
X Ray Diffraction 3.07 3.13 478 50 428 0.252 0.295 -- --
X Ray Diffraction 3.13 3.2 477 47 430 0.249 0.283 -- --
X Ray Diffraction 3.2 3.28 480 40 440 0.24 0.34 -- --
X Ray Diffraction 3.28 3.36 476 52 424 0.222 0.249 -- --
X Ray Diffraction 3.36 3.45 499 54 445 0.227 0.292 -- --
X Ray Diffraction 3.45 3.55 484 38 446 0.225 0.219 -- --
X Ray Diffraction 3.55 3.66 481 45 436 0.217 0.275 -- --
X Ray Diffraction 3.66 3.8 489 55 434 0.222 0.284 -- --
X Ray Diffraction 3.8 3.95 499 56 443 0.21 0.255 -- --
X Ray Diffraction 3.95 4.13 485 60 425 0.19 0.218 -- --
X Ray Diffraction 4.13 4.34 510 56 454 0.155 0.217 -- --
X Ray Diffraction 4.34 4.62 485 50 435 0.169 0.195 -- --
X Ray Diffraction 4.62 4.97 493 53 440 0.173 0.239 -- --
X Ray Diffraction 4.97 5.47 504 56 448 0.229 0.307 -- --
X Ray Diffraction 5.47 6.27 504 68 436 0.249 0.233 -- --
X Ray Diffraction 6.27 7.89 516 62 454 0.246 0.262 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 52.5
Anisotropic B[1][1] -5.74
Anisotropic B[1][2] 0.76
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -5.74
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 11.49
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 2.99
c_scbond_it 1.96
c_mcangle_it 2.73
c_mcbond_it 1.55
c_improper_angle_d 1.03
c_dihedral_angle_d 23.7
c_angle_deg 1.3
c_bond_d 0.007
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.32
Luzzati Sigma A (Observed) 0.34
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.41
Luzzati Sigma A (R-Free Set) 0.45
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2097
Nucleic Acid Atoms 0
Heterogen Atoms 20
Solvent Atoms 85

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
CNS Structure Solution
CNS 1.1 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 2.000 data extraction
CNS refinement
HKL data processing