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 MPD, 10mM Magnesium sulfate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 93.17 α = 90
b = 108.71 β = 90
c = 152.21 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 300 mm CCD -- 2008-04-04
Diffraction Radiation
Monochromator Protocol
Si(111) crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-ID 1.0000 APS 22-ID

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
1.81 42.84 98.9 0.058 -- -- 5.0 140976 139378 -- -3.0 33.25
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)
1.81 1.86 98.1 0.592 -- 2.61 5.0 --

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 1.81 42.84 -- -- -- 139376 6014 100.0 -- 0.21295 0.21134 0.24723 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 1.81 1.857 -- 505 9598 0.285 0.323 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 29.473
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_bond_refined_d 0.012
r_dihedral_angle_3_deg 14.124
r_scangle_it 3.601
r_mcangle_it 1.425
r_gen_planes_refined 0.006
r_scbond_it 2.219
r_angle_refined_deg 1.455
r_dihedral_angle_2_deg 33.434
r_mcbond_it 0.769
r_dihedral_angle_1_deg 5.517
r_dihedral_angle_4_deg 15.754
r_chiral_restr 0.094
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.137
Luzzati ESD (R-Free Set) 0.131
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9312
Nucleic Acid Atoms 848
Heterogen Atoms 119
Solvent Atoms 869

Software

Software
Software Name Purpose
XSCALE data scaling
REFMAC refinement
PDB_EXTRACT data extraction version: 3.005
SERGUI data collection version: sergui
XDS data reduction
AMoRE phasing