X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 8.5
Temperature 298.0
Details PEG8000, pH 8.5, vapor diffusion, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 122.19 α = 90
b = 79.66 β = 105.54
c = 125.91 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2008-12-16
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 0.979 EMBL/DESY, HAMBURG X12

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
2.1 121.3 98.4 0.085 0.085 -- 3.3 133960 133960 -- -- --
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)
2.1 2.21 94.2 0.561 0.561 1.4 3.3 18662

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 2.2 30.0 -- 0.0 -- 117344 5903 99.05 -- 0.2317 0.2281 0.3008 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 2.2 2.257 -- 428 7881 0.29 0.385 -- 95.47
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 49.3208
Anisotropic B[1][1] -0.37
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -2.33
Anisotropic B[2][2] 1.13
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.0
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.264
r_scbond_it 2.093
r_mcangle_it 1.469
r_mcbond_it 0.8
r_gen_planes_refined 0.007
r_chiral_restr 0.105
r_dihedral_angle_4_deg 23.53
r_dihedral_angle_3_deg 19.94
r_dihedral_angle_2_deg 38.723
r_dihedral_angle_1_deg 7.357
r_angle_refined_deg 1.613
r_bond_refined_d 0.014
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 15290
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 614

Software

Computing
Computing Package Purpose
MAR345dtb Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.5.0072 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 refinement
MOLREP molecular replacement
SCALA version: 3.2.21 data reduction
Mosflm data collection