X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.1
Temperature 293.0
Details 0.2 M Ammonium phosphate monobasic, 0.1 M Tris pH 8.5, 50% v/v (+/-)-2-Methyl-2,4-pentanediol, protein in 100 mM NaCl, 20 mM Tris, 1 mM DTT, pH 7.1. Protein 2 mg/mL, Mix 1.5 uL of protein and precipatant, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 59.08 α = 90
b = 44.57 β = 111.01
c = 67.72 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 ADSC QUANTUM 315 -- 2008-10-20
Diffraction Radiation
Monochromator Protocol
SI(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X29A 0.9792 NSLS X29A

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
1.59 33 91.692 -- -- -- -- 38536 38536 0.0 0.0 19.938
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)
1.593 1.634 75.34 -- -- -- -- 2312

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 1.59 33.0 -- 0.0 38536 38536 2057 91.69 -- 0.2123 0.21 0.25452 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 1.59 1.634 -- 111 2312 0.326 0.404 -- 75.34
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 21.764
Anisotropic B[1][1] 1.08
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.72
Anisotropic B[2][2] -0.53
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.04
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 5.562
r_scbond_it 3.548
r_mcangle_it 2.336
r_mcbond_it 1.423
r_gen_planes_refined 0.012
r_chiral_restr 0.143
r_dihedral_angle_4_deg 18.719
r_dihedral_angle_3_deg 14.004
r_dihedral_angle_2_deg 28.354
r_dihedral_angle_1_deg 6.349
r_angle_refined_deg 2.19
r_bond_refined_d 0.026
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2436
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 300

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
Molrep Structure Solution
REFMAC 5.5.0109 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.5.0109 refinement
Molrep model building
ADSC version: Quantum data collection