X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 277.0
Details 1.6M Ammonium sulfate, 10% Dioxane, 0.1M MES pH 6.5, Deoxy-Big Chap, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 164.3 α = 90
b = 36.98 β = 125.67
c = 99.43 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2005-11-02
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X25 0.960 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
2.49 50 99.3 0.134 -- -- 6.6 -- 17441 -- -1.0 --
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)
2.49 2.58 99.3 0.455 -- -- 4.7 1612

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 2.49 20.51 -- 0.0 17997 16380 1617 93.5 -- 0.2361 0.2305 0.2886 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 2.486 2.55 -- 96 963 0.371 0.459 -- 84.79
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 35.2124
Anisotropic B[1][1] -0.64
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.5
Anisotropic B[2][2] 0.23
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.0
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 1.793
r_nbd_refined 0.216
r_gen_planes_other 0.001
r_gen_planes_refined 0.004
r_chiral_restr 0.096
r_dihedral_angle_4_deg 16.232
r_dihedral_angle_3_deg 16.179
r_dihedral_angle_2_deg 35.579
r_dihedral_angle_1_deg 6.179
r_angle_other_deg 1.093
r_angle_refined_deg 1.401
r_bond_other_d 0.005
r_bond_refined_d 0.011
r_nbd_other 0.196
r_nbtor_refined 0.188
r_nbtor_other 0.086
r_xyhbond_nbd_refined 0.15
r_xyhbond_nbd_other 0.041
r_symmetry_vdw_refined 0.194
r_symmetry_vdw_other 0.174
r_symmetry_hbond_refined 0.16
r_mcbond_it 0.509
r_mcbond_other 0.082
r_mcangle_it 0.633
r_scbond_it 1.149
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2675
Nucleic Acid Atoms 226
Heterogen Atoms 87
Solvent Atoms 119

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
REFMAC5 version: 5.2.0019 refinement
SCALEPACK data reduction
DENZO data collection