X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Capillary Counterdiffusion
pH 5
Temperature 293.0
Details Sodium Formate, pH 5.0, Capillary Counterdiffusion, temperature 293.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 74.07 α = 90
b = 74.07 β = 90
c = 152.07 γ = 90
Symmetry
Space Group P 42 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 -- 2007-10-06
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE BM16 0.88560 ESRF BM16

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
2.15 20 99.4 0.07 0.07 -- 10.7 23741 23741 1.0 1.0 33.59
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)
2.15 2.23 100.0 0.367 -- -- 10.9 2339

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 2.15 19.942 -- 1.34 23658 23658 1214 99.42 0.192 0.192 0.1893 0.2451 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 2.15 2.236 -- 130 2468 0.2137 0.274 -- 100.0
X Ray Diffraction 2.236 2.3376 -- 143 2437 0.2141 0.3128 -- 100.0
X Ray Diffraction 2.3376 2.4607 -- 141 2434 0.205 0.2681 -- 100.0
X Ray Diffraction 2.4607 2.6145 -- 134 2472 0.2029 0.2749 -- 100.0
X Ray Diffraction 2.6145 2.8159 -- 123 2492 0.2153 0.2952 -- 100.0
X Ray Diffraction 2.8159 3.0983 -- 147 2487 0.205 0.2756 -- 100.0
X Ray Diffraction 3.0983 3.5444 -- 144 2501 0.1847 0.2353 -- 100.0
X Ray Diffraction 3.5444 4.4574 -- 135 2531 0.1517 0.1833 -- 99.0
X Ray Diffraction 4.4574 19.9433 -- 117 2622 0.1864 0.2319 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 40.1398
Anisotropic B[1][1] 3.3967
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 3.3967
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -6.7933
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.018
f_chiral_restr 0.068
f_plane_restr 0.004
f_angle_d 1.057
f_dihedral_angle_d 15.582
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2388
Nucleic Acid Atoms 0
Heterogen Atoms 96
Solvent Atoms 160

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
MOLREP phasing
PHENIX refinement version: 1.6.1_357
PDB_EXTRACT data extraction version: 3.10
HKL-2000 data collection