X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.9
Temperature 293.0
Details 0.1 M sodium cacodylate, 0.2 M magnesium sulfate, 10-12% PEG 8000; protein concentration 13.6 mg/ml, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 83.93 α = 90
b = 51.38 β = 95.66
c = 108.87 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 -- 2004-01-01
Diffraction Radiation
Monochromator Protocol
graphite SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X29A 1.1 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
1.75 30 96.7 0.093 9.3 -- 3.3 93625 90611 0.0 -3.0 --
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)
1.75 1.81 86.7 0.427 0.427 2.26 2.6 8020

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 1.75 30.0 0.0 0.0 93598 90462 9050 96.65 -- 0.23222 0.22764 0.27373 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 1.75 1.81 7809 792 7017 0.303 0.381 -- 86.13
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 15.731
Anisotropic B[1][1] -0.96
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.09
Anisotropic B[2][2] 1.29
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.31
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.483
r_scbond_it 1.579
r_mcangle_it 1.378
r_mcbond_it 0.842
r_nbd_refined 0.21
r_gen_planes_refined 0.003
r_chiral_restr 0.07
r_dihedral_angle_4_deg 14.27
r_dihedral_angle_3_deg 12.727
r_dihedral_angle_2_deg 35.185
r_dihedral_angle_1_deg 6.402
r_angle_refined_deg 0.963
r_bond_refined_d 0.008
r_nbtor_refined 0.319
r_xyhbond_nbd_refined 0.156
r_metal_ion_refined 0.189
r_symmetry_vdw_refined 0.264
r_symmetry_hbond_refined 0.186
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7481
Nucleic Acid Atoms 0
Heterogen Atoms 7
Solvent Atoms 1166

Software

Computing
Computing Package Purpose
ADSC QUANTUM Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0019 refinement