X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 3.5
Temperature 293.0
Details 0.1M citric acid 2M (NH4)2SO4, pH 3.5, vapor diffusion, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 103.68 α = 90
b = 103.68 β = 90
c = 106.54 γ = 120
Symmetry
Space Group P 31 1 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2008-09-25
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID29 0.9814 ESRF ID29

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
2.3 89.8 99.4 0.081 0.081 -- 7.4 29100 29100 -- -- 46.27
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)
2.3 2.42 98.8 0.519 0.519 1.4 7.5 4176

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 2.3 20.0 -- 0.0 29019 27545 1474 99.36 -- 0.1891 0.1871 0.2259 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 2.3 2.359 -- 100 1999 0.232 0.292 -- 98.87
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 45.9823
Anisotropic B[1][1] -0.05
Anisotropic B[1][2] -0.03
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.05
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.08
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.291
r_scbond_it 1.567
r_mcangle_it 0.88
r_mcbond_it 0.593
r_symmetry_hbond_refined 0.178
r_bond_refined_d 0.012
r_angle_refined_deg 1.45
r_dihedral_angle_1_deg 6.485
r_dihedral_angle_2_deg 35.169
r_dihedral_angle_3_deg 17.457
r_dihedral_angle_4_deg 16.984
r_chiral_restr 0.095
r_gen_planes_refined 0.004
r_nbd_refined 0.199
r_nbtor_refined 0.305
r_xyhbond_nbd_refined 0.127
r_symmetry_vdw_refined 0.219
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3497
Nucleic Acid Atoms 0
Heterogen Atoms 235
Solvent Atoms 89

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
REFMAC5 refinement
MOLREP molecular replacement
SCALA version: 3.2.25 data reduction
Mosflm data collection