X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Temperature 293.0
Details 100mM Bis-tris, 200mM LiSO4, 16-20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 59.98 α = 90
b = 180.53 β = 90
c = 78.33 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2008-09-26
Diffraction Radiation
Monochromator Protocol
DCM SI(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON LNLS BEAMLINE W01B-MX2 -- LNLS W01B-MX2

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
2.3 180.53 93.3 0.103 0.103 -- 3.4 -- 35871 -- 2.0 --
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)
2.3 2.42 88.6 0.552 0.552 1.4 3.4 --

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 2.3 49.958 -- 1.35 38633 35822 1788 92.64 -- 0.2092 0.208 0.2302 --
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 2.3 2.3622 -- 127 2422 0.2682 0.2864 -- 88.0
X Ray Diffraction 2.3622 2.4317 -- 122 2478 0.258 0.3301 -- 88.0
X Ray Diffraction 2.4317 2.5102 -- 130 2467 0.2581 0.2995 -- 89.0
X Ray Diffraction 2.5102 2.5999 -- 124 2503 0.246 0.2749 -- 89.0
X Ray Diffraction 2.5999 2.704 -- 143 2485 0.2374 0.2546 -- 90.0
X Ray Diffraction 2.704 2.8271 -- 136 2537 0.247 0.3022 -- 91.0
X Ray Diffraction 2.8271 2.9761 -- 124 2587 0.2414 0.2603 -- 92.0
X Ray Diffraction 2.9761 3.1625 -- 148 2601 0.2343 0.2453 -- 93.0
X Ray Diffraction 3.1625 3.4067 -- 151 2660 0.2201 0.2573 -- 95.0
X Ray Diffraction 3.4067 3.7494 -- 160 2748 0.1977 0.1932 -- 98.0
X Ray Diffraction 3.7494 4.2917 -- 149 2827 0.1777 0.184 -- 99.0
X Ray Diffraction 4.2917 5.406 -- 145 2837 0.1592 0.2019 -- 98.0
X Ray Diffraction 5.406 49.9702 -- 129 2882 0.1967 0.2092 -- 94.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 43.24
Anisotropic B[1][1] 19.2487
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -13.0254
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -6.0073
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.002
f_chiral_restr 0.042
f_dihedral_angle_d 11.53
f_angle_d 0.573
f_bond_d 0.002
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5244
Nucleic Acid Atoms 0
Heterogen Atoms 86
Solvent Atoms 184

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.8_1069) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
DM density modification
Phaser molecular replacement
SCALA version: 3.2.25 data reduction
Mosflm data collection