X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.5
Temperature 293.0
Details 0.1M sodium acetate pH 4.5, 2.5M sodium chloride, 0.2M lithium sulfate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.04 α = 90
b = 93.18 β = 90
c = 105.44 γ = 90
Symmetry
Space Group I 2 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD double crystal monochromator 2010-05-13
Diffraction Radiation
Monochromator Protocol
double crystal MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 0.91162, 0.97934, 0.97915 SSRL BL9-2

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
1.9 29.79 99.9 -- 0.063 7.675 3.7 21347 21347 -- -- --
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)
1.9 1.95 100.0 0.758 0.758 1.7 3.7 1573

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
MAD 1.9 29.794 -- 0.0 -- 21345 1097 99.63 -- 0.1629 0.1616 0.1873 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 1.9 1.949 -- 71 1495 0.291 0.296 -- 99.81
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 44.9133
Anisotropic B[1][1] -0.87
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.64
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.77
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_it 5.983
r_mcangle_it 5.652
r_mcbond_other 4.165
r_bond_refined_d 0.011
r_bond_other_d 0.001
r_angle_refined_deg 1.404
r_angle_other_deg 0.729
r_dihedral_angle_1_deg 5.483
r_dihedral_angle_2_deg 39.26
r_dihedral_angle_3_deg 14.245
r_dihedral_angle_4_deg 14.652
r_chiral_restr 0.07
r_gen_planes_refined 0.005
r_gen_planes_other 0.001
r_mcbond_it 4.167
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1592
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 101

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
SHELXD,SHARP Structure Solution
REFMAC 5.7.0032 Structure Refinement
Software
Software Name Purpose
REFMAC5 version: 5.7.0032 refinement
SCALA version: 3.3.15 phasing
SHARP phasing
SHELX phasing
pdb_extract version: 3.10 data extraction
MOLPROBITY version: 3beta29 validation