X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 298.0
Details 1.6M AMMONIUM SULFATE, 4% PEG400, 0.1M HEPES PH7.5, NITROGEN ATMOSPHERE, 20MG/ML PROTEIN WITH 1MM FE(II), 2.0MM 2OG AND 10MM PEPTIDE , VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 86.34 α = 90
b = 86.34 β = 90
c = 146.45 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2006-02-02
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SRS BEAMLINE PX14.2 0.979 SRS PX14.2

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
2.6 40 99.3 -- 0.078 -- 3.4 -- 16449 -- 1.0 47.8
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)
2.6 2.69 99.9 -- 0.59 2.1 3.5 1739

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
FOURIER SYNTHESIS 2.6 34.15 -- 0.0 -- 16449 1617 92.9 -- -- 0.208 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 2.6 2.63 -- 41 378 0.315 0.3887 -- --
X Ray Diffraction 2.63 2.66 -- 41 419 0.3374 0.3754 -- --
X Ray Diffraction 2.66 2.69 -- 46 406 0.3165 0.4048 -- --
X Ray Diffraction 2.69 2.72 -- 46 419 0.2919 0.362 -- --
X Ray Diffraction 2.72 2.75 -- 39 408 0.3044 0.3207 -- --
X Ray Diffraction 2.75 2.79 -- 43 435 0.2604 0.3994 -- --
X Ray Diffraction 2.79 2.82 -- 33 432 0.274 0.3081 -- --
X Ray Diffraction 2.82 2.86 -- 44 440 0.2759 0.2893 -- --
X Ray Diffraction 2.86 2.9 -- 41 462 0.2648 0.3823 -- --
X Ray Diffraction 2.9 2.95 -- 45 440 0.2224 0.2511 -- --
X Ray Diffraction 2.95 2.99 -- 61 464 0.2551 0.314 -- --
X Ray Diffraction 2.99 3.04 -- 48 431 0.2308 0.2862 -- --
X Ray Diffraction 3.04 3.09 -- 51 455 0.2629 0.3391 -- --
X Ray Diffraction 3.09 3.15 -- 46 458 0.2231 0.2736 -- --
X Ray Diffraction 3.15 3.21 -- 50 473 0.2204 0.3271 -- --
X Ray Diffraction 3.21 3.28 -- 46 460 0.2208 0.3241 -- --
X Ray Diffraction 3.28 3.35 -- 64 459 0.2224 0.2613 -- --
X Ray Diffraction 3.35 3.42 -- 53 467 0.2206 0.321 -- --
X Ray Diffraction 3.42 3.51 -- 48 489 0.1787 0.247 -- --
X Ray Diffraction 3.51 3.61 -- 39 490 0.1786 0.2179 -- --
X Ray Diffraction 3.61 3.71 -- 61 472 0.1871 0.2306 -- --
X Ray Diffraction 3.71 3.83 -- 65 459 0.1966 0.2261 -- --
X Ray Diffraction 3.83 3.97 -- 53 486 0.1832 0.2534 -- --
X Ray Diffraction 3.97 4.13 -- 60 486 0.1557 0.1887 -- --
X Ray Diffraction 4.13 4.32 -- 53 488 0.1605 0.1963 -- --
X Ray Diffraction 4.32 4.54 -- 43 507 0.1625 0.233 -- --
X Ray Diffraction 4.54 4.83 -- 54 497 0.1657 0.232 -- --
X Ray Diffraction 4.83 5.2 -- 71 473 0.1638 0.2246 -- --
X Ray Diffraction 5.2 5.72 -- 55 510 0.2107 0.2435 -- --
X Ray Diffraction 5.72 6.55 -- 59 509 0.2236 0.2675 -- --
X Ray Diffraction 6.55 8.25 -- 60 515 0.2238 0.2449 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 60.8028
Anisotropic B[1][1] -6.17
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -6.17
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 12.35
RMS Deviations
Key Refinement Restraint Deviation
c_mcangle_it 2.4
c_mcbond_it 1.4
c_improper_angle_d 0.82
c_scangle_it 2.92
c_angle_deg 1.3
c_dihedral_angle_d 23.8
c_bond_d 0.007
c_scbond_it 1.91
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.3
Luzzati Sigma A (Observed) 0.39
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.4
Luzzati Sigma A (R-Free Set) 0.49
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2795
Nucleic Acid Atoms 0
Heterogen Atoms 39
Solvent Atoms 163

Software

Software
Software Name Purpose
DENZO data reduction
CNS refinement version: 1.1
PDB_EXTRACT data extraction version: 3.10
ADSC data collection version: Quantum
HKL-2000 data scaling
CNS phasing