X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.8
Temperature 290.0
Details 50% Saturated ammonium sulfate, 0.1M MES, 2.5% v/v Methylpentanediol, 10mM Magnesium sulfate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 93.28 α = 90
b = 108.79 β = 90
c = 152.09 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 -- 2008-08-01
Diffraction Radiation
Monochromator Protocol
Si(111) crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-BM 0.97121 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
1.7 46.98 99.8 0.06 -- -- 3.9 169954 169685 -- -3.0 26.76
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)
1.7 1.74 99.8 0.561 -- 2.5 3.9 --

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 1.7 46.98 -- 0.0 169685 169684 7528 100.0 -- 0.2114 0.20974 0.24686 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 1.7 1.744 -- 619 11768 0.291 0.33 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 23.552
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.111
r_scbond_it 1.918
r_mcangle_it 1.243
r_mcbond_it 0.653
r_gen_planes_refined 0.005
r_chiral_restr 0.083
r_dihedral_angle_4_deg 16.14
r_dihedral_angle_3_deg 14.151
r_dihedral_angle_2_deg 33.114
r_dihedral_angle_1_deg 5.306
r_angle_refined_deg 1.325
r_bond_refined_d 0.01
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.113
Luzzati ESD (R-Free Set) 0.113
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9292
Nucleic Acid Atoms 848
Heterogen Atoms 170
Solvent Atoms 996

Software

Computing
Computing Package Purpose
SER-CAT sergui Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
REFMAC 5.5.0070 Structure Solution
REFMAC 5.5.0070 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.005 data extraction
REFMAC5 refinement
Xscale data processing