X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.8
Temperature 293.0
Details 2.8M Na/K phosphate buffer, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 107.66 α = 90
b = 63.08 β = 111.75
c = 54.04 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 298
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH Monochromator 2003-10-08
Diffraction Radiation
Monochromator Protocol
M SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 1.5418 -- --

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
3 30 79.01 0.161 -- -- 4.1 5406 5387 2.0 2.0 --
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)
3.002 3.079 34.3 0.43 -- -- -- 584

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 3.0 21.18 -- 2.0 5387 5133 254 79.01 0.1857 0.1857 0.18072 0.28524 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 3.002 3.079 137 10 137 0.299 0.513 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 33.322
Anisotropic B[1][1] -0.11
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.12
Anisotropic B[2][2] -0.04
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.06
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_vdw_other 0.292
r_symmetry_vdw_refined 0.306
r_chiral_restr 0.131
r_gen_planes_refined 0.01
r_mcangle_it 2.321
r_gen_planes_other 0.005
r_nbtor_other 0.12
r_symmetry_hbond_refined 0.057
r_bond_refined_d 0.041
r_angle_other_deg 1.512
r_mcbond_it 1.218
r_nbd_other 0.285
r_bond_other_d 0.002
r_xyhbond_nbd_refined 0.21
r_nbd_refined 0.293
r_scangle_it 5.571
r_scbond_it 3.22
r_angle_refined_deg 3.149
r_dihedral_angle_1_deg 11.291
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2200
Nucleic Acid Atoms 0
Heterogen Atoms 86
Solvent Atoms 0

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.24
MAR data reduction
SCALEPACK data scaling
AMoRE phasing