X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.9
Temperature 277.0
Details 0.2 M Ammonium Sulfate, 32% w/v PEG 4000, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 57.63 α = 90
b = 67.25 β = 90
c = 69 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD Rosenbaum-Rock double-crystal monochromator: sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror 2010-03-14
Diffraction Radiation
Monochromator Protocol
double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-BM 0.91339 APS 22-BM

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
1.44 35 98.98 0.089 -- -- 3.6 46777 46300 -- 2.0 8.2
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)
1.44 1.447 98.61 0.413 -- 2.69 3.5 3423

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 1.44 35.0 2.0 -- 46777 46300 2454 98.98 -- 0.20463 0.20312 0.23329 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 1.44 1.477 3375 167 3375 0.365 0.368 -- 98.61
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Anisotropic
Mean Isotropic B 8.181
Anisotropic B[1][1] -0.12
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.51
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.63
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 4.253
r_sphericity_free 18.335
r_bond_refined_d 0.008
r_bond_other_d 0.001
r_angle_refined_deg 2.498
r_angle_other_deg 0.859
r_dihedral_angle_1_deg 4.999
r_dihedral_angle_2_deg 38.418
r_dihedral_angle_3_deg 14.893
r_dihedral_angle_4_deg 18.485
r_chiral_restr 0.072
r_gen_planes_refined 0.008
r_gen_planes_other 0.004
r_rigid_bond_restr 1.631
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2181
Nucleic Acid Atoms 0
Heterogen Atoms 129
Solvent Atoms 238

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.6.0117 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.6.0117 refinement
PHASER model building
HKL-2000 data collection