X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.1
Temperature 298.0
Details 10% PEG-3350, 100 mM Ca(OAc)2, 100 mM HEPES, 2.5% Glycerol, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 124.48 α = 90
b = 124.48 β = 90
c = 70.47 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 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
2.21 30 97.4 0.051 -- -- 9.7 28140 27408 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)
2.22 2.26 79.9 0.353 -- 2.2 3.8 1092

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 2.215 28.468 -- 1.49 -- 27377 1365 97.41 -- 0.2145 0.2117 0.2691 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 2.215 2.2939 -- 110 2190 0.3062 0.322 -- 83.0
X Ray Diffraction 2.2939 2.3857 -- 136 2522 0.3075 0.3583 -- 97.0
X Ray Diffraction 2.3857 2.4943 -- 137 2604 0.2907 0.3747 -- 99.0
X Ray Diffraction 2.4943 2.6257 -- 135 2620 0.2776 0.335 -- 99.0
X Ray Diffraction 2.6257 2.7901 -- 139 2621 0.27 0.3661 -- 99.0
X Ray Diffraction 2.7901 3.0053 -- 139 2633 0.2442 0.303 -- 100.0
X Ray Diffraction 3.0053 3.3073 -- 139 2668 0.2133 0.3028 -- 100.0
X Ray Diffraction 3.3073 3.7849 -- 141 2675 0.1959 0.2616 -- 100.0
X Ray Diffraction 3.7849 4.7649 -- 143 2718 0.1685 0.211 -- 100.0
X Ray Diffraction 4.7649 28.4707 -- 146 2761 0.1906 0.2378 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 5.2801
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 5.2801
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -10.5602
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.075
f_dihedral_angle_d 18.769
f_angle_d 1.227
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2693
Nucleic Acid Atoms 466
Heterogen Atoms 1
Solvent Atoms 74

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