X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.6
Temperature 294.0
Details sodium acetate, PEG4000, ammonium acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 100.73 α = 90
b = 48.68 β = 120.82
c = 74.69 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2001-10-18
Diffraction Radiation
Monochromator Protocol
-- MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X9B 0.97946, 0.97133, 0.97900 NSLS X9B

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
1.94 30 99.4 0.073 -- -- 11.0 -- 23111 -- -3.0 28.0
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)
1.94 2.01 94.8 0.342 -- 5.8 -- 2170

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
MAD 1.94 30.0 -- -- -- 21926 1182 99.7 -- 0.18641 0.18424 0.2268 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 1.94 1.99 -- 79 1560 0.24 0.252 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model TLS
Mean Isotropic B 21.106
Anisotropic B[1][1] -1.58
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.62
Anisotropic B[2][2] 0.05
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.16
RMS Deviations
Key Refinement Restraint Deviation
r_nbtor_other 0.094
r_nbd_other 0.267
r_nbd_refined 0.247
r_gen_planes_other 0.004
r_gen_planes_refined 0.008
r_chiral_restr 0.127
r_dihedral_angle_1_deg 7.542
r_angle_other_deg 0.874
r_angle_refined_deg 1.803
r_bond_other_d 0.001
r_bond_refined_d 0.015
r_xyhbond_nbd_refined 0.212
r_symmetry_vdw_refined 0.134
r_symmetry_vdw_other 0.328
r_symmetry_hbond_refined 0.3
r_mcbond_it 1.902
r_mcangle_it 3.06
r_scbond_it 5.018
r_scangle_it 7.528
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.246
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2454
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 254

Software

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