1SI3

Crystal structure of the PAZ domain of human eIF2c1 in complex with a 9-mer siRNA-like duplex


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.6
Temperature 293.0
Details PEG 1000, POTASSIUM CHLORIDE, HEPES-NAOH, DITHIOTHREITOL, pH 7.60, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 99.8 α = 90
b = 99.8 β = 90
c = 34.93 γ = 120
Symmetry
Space Group P 64

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 2003-10-18
Diffraction Radiation
Monochromator Protocol
SI 111 SAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-BM 0.9796 APS 19-BM

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
2.6 20 99.9 -- 0.115 -- 12.6 -- 6431 -- -3.0 59.2
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)
2.6 2.69 100.0 -- 0.663 3.4 -- --

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
SAD 2.6 19.83 -- 0.0 6310 5908 593 93.6 0.253 0.247 0.247 0.304 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 2.6 2.69 -- 58 503 0.396 0.501 0.066 89.8
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 58.9
Anisotropic B[1][1] 3.73
Anisotropic B[1][2] 4.9
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 3.73
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -7.47
RMS Deviations
Key Refinement Restraint Deviation
c_mcangle_it 2.77
c_bond_d 0.008
c_mcbond_it 1.6
c_scangle_it 3.0
c_scbond_it 1.9
c_angle_deg 1.2
c_dihedral_angle_d 21.0
c_improper_angle_d 1.17
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.41
Luzzati Sigma A (Observed) 0.48
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.59
Luzzati Sigma A (R-Free Set) 0.58
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 977
Nucleic Acid Atoms 185
Heterogen Atoms 0
Solvent Atoms 15

Software

Software
Software Name Purpose
HKL-2000 data collection
SCALEPACK data scaling
CNS refinement version: 1.1
HKL-2000 data reduction
CNS phasing version: 1.1