X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.3
Temperature 293.0
Details PEG 4000, potassium dihydrophosphate, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 43.01 α = 109.29
b = 46.84 β = 95.45
c = 55.7 γ = 116.68
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 2001-05-18
Diffraction Radiation
Monochromator Protocol
undulator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.50000 SPRING-8 BL41XU

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
1.1 36.79 98.1 0.042 0.042 -- 1.9 139823 139823 0.0 0.0 5.943
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)
1.1 1.13 97.2 0.248 0.248 2.4 1.9 10242

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 1.1 36.793 0.0 0.0 139823 139823 7125 98.1 0.11735 0.11735 0.11628 0.13719 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 1.1 1.129 9684 545 9684 0.178 0.212 -- 95.8
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model anisotropic
Mean Isotropic B 8.354
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.831
r_nbd_other 0.466
r_mcangle_it 1.573
r_gen_planes_refined 0.008
r_gen_planes_other 0.002
r_dihedral_angle_3_deg 16.2
r_dihedral_angle_1_deg 5.181
r_chiral_restr 0.103
r_bond_refined_d 0.012
r_bond_other_d 0.002
r_angle_refined_deg 1.675
r_angle_other_deg 0.864
r_nbtor_other 1.137
r_scangle_it 2.764
r_mcbond_it 1.077
r_scbond_it 1.966
r_rigid_bond_restr 1.17
r_sphericity_bonded 2.237
r_sphericity_free 2.912
r_symmetry_hbond_refined 0.166
r_symmetry_vdw_other 0.304
r_symmetry_vdw_refined 0.293
r_xyhbond_nbd_refined 0.17
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3221
Nucleic Acid Atoms 0
Heterogen Atoms 66
Solvent Atoms 770

Software

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