X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.8
Temperature 303.0
Details ammonium sulfate, NaI, MES, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 303K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 53.87 α = 90
b = 62.84 β = 101.02
c = 107.21 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 98
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU JUPITER 210 mirrors 2002-02-23
Diffraction Radiation
Monochromator Protocol
Diamond SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL45PX -- SPRING-8 BL45PX

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
1.5 44 99.0 0.064 0.064 -- 2.3 -- 110939 -- 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)
1.5 1.58 98.7 0.306 0.306 2.2 2.3 --

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
MR 1.5 12.0 -- -- 66791 105106 5579 98.89 -- 0.178 0.177 0.202 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 1.5 1.54 -- 407 7584 0.212 0.266 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 16.11
Anisotropic B[1][1] -0.05
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.027
Anisotropic B[2][2] -0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.026
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 2.538
r_nbd_other 0.184
r_nbd_refined 0.233
r_gen_planes_other 0.002
r_gen_planes_refined 0.006
r_chiral_restr 0.085
r_dihedral_angle_2_deg 11.668
r_dihedral_angle_1_deg 3.064
r_angle_other_deg 0.833
r_angle_refined_deg 1.709
r_bond_other_d 0.001
r_bond_refined_d 0.015
r_xyhbond_nbd_refined 0.161
r_xyhbond_nbd_other 0.008
r_symmetry_vdw_refined 0.242
r_symmetry_vdw_other 0.226
r_symmetry_hbond_refined 0.114
r_mcbond_it 1.179
r_mcangle_it 1.902
r_scbond_it 2.724
r_scangle_it 4.211
r_rigid_bond_restr 1.468
r_sphericity_free 3.453
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5005
Nucleic Acid Atoms 0
Heterogen Atoms 202
Solvent Atoms 584

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement
AMORE model building
SCALA data reduction
MOSFLM data collection