X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 293.0
Details 1.0M AMMONIUM SULFATE, 0.2M BICINE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 50.95 α = 90
b = 55.6 β = 115.81
c = 53.13 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 RAYONIX MX225HE mirrors 2011-05-18
Diffraction Radiation
Monochromator Protocol
Rotated-inclined double-crystal monochromator , Si (111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.90 SPRING-8 BL41XU

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
1.15 50 95.9 -- 0.069 -- 3.6 94807 90920 0.0 0.0 --
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)
1.15 1.19 93.1 -- 0.535 2.9 3.1 8782

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 1.15 47.83 -- -- -- 86188 4538 95.74 -- 0.13313 0.13159 0.1621 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 1.15 1.18 6117 312 6117 0.195 0.239 -- 91.82
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 13.826
Anisotropic B[1][1] -0.03
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.01
Anisotropic B[2][2] 0.1
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.08
RMS Deviations
Key Refinement Restraint Deviation
r_rigid_bond_restr 3.393
r_scangle_it 8.614
r_scbond_it 6.304
r_mcangle_it 4.023
r_mcbond_it 2.851
r_gen_planes_refined 0.009
r_chiral_restr 0.089
r_dihedral_angle_4_deg 14.474
r_dihedral_angle_3_deg 12.43
r_dihedral_angle_2_deg 35.376
r_dihedral_angle_1_deg 5.995
r_angle_refined_deg 1.639
r_bond_refined_d 0.012
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2070
Nucleic Acid Atoms 0
Heterogen Atoms 24
Solvent Atoms 304

Software

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