X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.65
Temperature 298.0
Details 10.5% PEG 550 MME, 10 mM Phenol, 0.1 M sodium acetate, pH 4.65, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 53.35 α = 90
b = 75.32 β = 106.29
c = 61.78 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 MAR CCD 165 mm -- 2007-04-26
Diffraction Radiation
Monochromator Protocol
Double crystal monochromator with fixed exit geometry; Bragg angle range is 7.55 degrees - 28 degrees; sagitally focusing Si(111) crystals SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X3A 0.97561 NSLS X3A

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
1.58 30 98.4 -- 0.061 -- 7.3 62650 62650 1.0 1.0 --
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)
1.6 1.66 97.6 -- 0.329 5.7 7.4 --

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 1.58 29.5 -- -- 62650 59447 3175 96.86 -- 0.19246 0.19139 0.21252 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 1.576 1.617 -- 191 3453 0.237 0.267 -- 76.68
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 22.033
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_4_deg 10.178
r_bond_refined_d 0.007
r_angle_refined_deg 1.073
r_chiral_restr 0.073
r_scangle_it 2.583
r_dihedral_angle_1_deg 5.848
r_dihedral_angle_2_deg 32.692
r_gen_planes_refined 0.004
r_mcbond_it 0.487
r_mcangle_it 0.977
r_dihedral_angle_3_deg 12.174
r_scbond_it 1.644
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3511
Nucleic Acid Atoms 0
Heterogen Atoms 25
Solvent Atoms 490

Software

Software
Software Name Purpose
CBASS data collection
HKL2Map model building
REFMAC refinement version: 5.5.0072
HKL-2000 data reduction
HKL-2000 data scaling
HKL2Map phasing