X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.9
Temperature 277.0
Details PEG 3350, magnesium formate, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 97.16 α = 90
b = 189.33 β = 90
c = 45.76 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2002-12-18
Diffraction Radiation
Monochromator Protocol
osmic SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 5.0.3 1.00 ALS 5.0.3

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
1.2 95.35 95.0 -- -- -- -- 123103 116923 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)
1.2 1.24 93.4 -- -- -- -- --

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 1.2 35.28 -- 0.0 123103 116923 6170 93.34 -- 0.1721 0.17098 0.19511 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 1.2 1.231 -- 307 5658 0.247 0.251 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 12.006
Anisotropic B[1][1] -0.05
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.58
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.62
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 1.313
r_sphericity_free 1.277
r_rigid_bond_restr 0.676
r_scangle_it 2.26
r_scbond_it 1.374
r_mcangle_it 1.003
r_mcbond_it 0.578
r_symmetry_hbond_refined 0.082
r_symmetry_vdw_other 0.267
r_symmetry_vdw_refined 0.126
r_bond_refined_d 0.006
r_bond_other_d 0.002
r_angle_refined_deg 1.094
r_angle_other_deg 0.755
r_dihedral_angle_1_deg 5.805
r_chiral_restr 0.068
r_gen_planes_refined 0.004
r_gen_planes_other 0.003
r_nbd_refined 0.201
r_nbd_other 0.227
r_nbtor_other 0.08
r_xyhbond_nbd_refined 0.076
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2492
Nucleic Acid Atoms 0
Heterogen Atoms 10
Solvent Atoms 612

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
CCP4 (TRUNCATE) Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement