X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 298.0
Details 10% PEG-3350, 100 mM Ca(OAc)2, 100 mM HEPES, 2.5% Glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 50.97 α = 75.6
b = 51.2 β = 82.97
c = 98.84 γ = 70.14
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2007-10-18
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X25 0.9795 NSLS X25

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 30 81.1 0.03 -- -- 1.8 25946 21042 0.0 0.0 --
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 2.34 50.5 0.19 -- 2.0 1.4 947

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 2.305 27.065 -- 2.21 -- -- 1589 80.8 -- 0.1883 0.1847 0.26 --
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 2.3046 2.379 -- 94 1801 0.2925 0.4181 -- 52.0
X Ray Diffraction 2.379 2.4639 -- 106 2211 0.2579 0.3064 -- 63.0
X Ray Diffraction 2.4639 2.5625 -- 127 2449 0.2351 0.3174 -- 70.0
X Ray Diffraction 2.5625 2.679 -- 132 2532 0.2449 0.3155 -- 73.0
X Ray Diffraction 2.679 2.8201 -- 147 2680 0.2535 0.3382 -- 78.0
X Ray Diffraction 2.8201 2.9966 -- 141 2920 0.2557 0.3188 -- 83.0
X Ray Diffraction 2.9966 3.2276 -- 158 3055 0.2257 0.3287 -- 89.0
X Ray Diffraction 3.2276 3.5518 -- 168 3232 0.1887 0.2627 -- 94.0
X Ray Diffraction 3.5518 4.0643 -- 167 3310 0.1689 0.2478 -- 96.0
X Ray Diffraction 4.0643 5.1149 -- 176 3388 0.1424 0.2063 -- 97.0
X Ray Diffraction 5.1149 27.0673 -- 173 3276 0.1605 0.2355 -- 95.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 2.1877
Anisotropic B[1][2] 2.6214
Anisotropic B[1][3] 2.4321
Anisotropic B[2][2] 1.3028
Anisotropic B[2][3] 1.8895
Anisotropic B[3][3] -3.4905
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.076
f_dihedral_angle_d 18.282
f_angle_d 1.142
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5440
Nucleic Acid Atoms 997
Heterogen Atoms 3
Solvent Atoms 91

Software

Computing
Computing Package Purpose
CBASS Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASER in PHENIX Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.3_928) refinement
PHASER version: in PHENIX model building
CBASS data collection