X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 6.8
Details 10% PEG 3350, NAF, PH 7.0, VAPOUR DIFFUSION, HANGING DROP, TEMPERATURE 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 53.37 α = 90
b = 70.75 β = 90
c = 72.18 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE (RAXIS IV) RIGAKU MIRRORS 2004-12-01
Diffraction Radiation
Monochromator Protocol
NI FILTER SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-D -- -- --

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
1.8 29.9 99.3 0.04 -- -- 3.43 -- 25793 -- 2.8 --
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)
1.8 1.86 97.5 0.37 -- 2.8 2.67 --

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 1.8 29.0 -- -- -- 24966 826 99.3 -- 0.18 0.178 0.231 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 1.8 1.85 -- 45 1776 0.26 0.304 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 36.23
Anisotropic B[1][1] 0.45
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.44
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.88
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 8.388
r_scbond_it 6.469
r_mcangle_it 4.256
r_mcbond_it 3.613
r_nbd_refined 0.295
r_gen_planes_other 0.001
r_gen_planes_refined 0.015
r_chiral_restr 0.136
r_dihedral_angle_4_deg 24.552
r_dihedral_angle_3_deg 21.775
r_dihedral_angle_2_deg 42.006
r_dihedral_angle_1_deg 8.342
r_angle_other_deg 1.266
r_angle_refined_deg 1.994
r_bond_other_d 0.001
r_bond_refined_d 0.011
r_nbd_other 0.256
r_nbtor_refined 0.197
r_nbtor_other 0.102
r_xyhbond_nbd_refined 0.293
r_symmetry_vdw_refined 0.267
r_symmetry_vdw_other 0.284
r_symmetry_hbond_refined 0.294
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2357
Nucleic Acid Atoms 0
Heterogen Atoms 16
Solvent Atoms 253

Software

Computing
Computing Package Purpose
D*TREK Data Reduction (intensity integration)
D*TREK Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.2.0005 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0005 refinement
MOLREP model building