X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.5
Temperature 288.0
Details 100 mM sodium citrate, 100 mM MgCl2 and 35% PEG 400, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 288K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 61.41 α = 90
b = 61.41 β = 90
c = 145.01 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- 2003-01-05
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU 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
2.5 30 99.9 0.081 -- -- 4.9 11523 11512 -- 3.1 55.4
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)
2.5 2.64 99.9 0.478 -- 3.1 5.0 --

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 2.5 30.0 3.1 1.55 -- 10957 553 99.84 -- 0.21569 0.21338 0.26203 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 2.5 2.565 -- 49 775 0.285 0.324 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 42.167
Anisotropic B[1][1] -0.2
Anisotropic B[1][2] -0.1
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.2
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.3
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.021
r_gen_planes_other 0.004
r_symmetry_vdw_other 0.276
r_scangle_it 4.19
r_nbd_refined 0.194
r_angle_other_deg 0.941
r_symmetry_hbond_refined 0.066
r_scbond_it 2.37
r_symmetry_vdw_refined 0.22
r_mcbond_it 1.022
r_xyhbond_nbd_refined 0.22
r_bond_other_d 0.002
r_angle_refined_deg 1.815
r_dihedral_angle_1_deg 7.587
r_chiral_restr 0.096
r_gen_planes_refined 0.007
r_nbd_other 0.238
r_nbtor_other 0.095
r_mcangle_it 1.919
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2380
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 66

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
SCALA data reduction
MOSFLM data collection
AMoRE model building
REFMAC version: 5.1.24 refinement