Experiment: 2AVD

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1SUI	PDB entry 1sui

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	300	PEG 3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.431

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.882	α = 90
b = 65.222	β = 102.66
c = 61.799	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV		2005-08-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54

Data Collection

Overall
ID #	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	1.7	60.3	94.4	0.054	0.054	10.4	3.7	41907	41907			20.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.7	1.76	72.3		0.41	0.41	2	3	3185

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1sui	1.7	60.3	39767	39767	2122	94.33	0.17357	0.17357	0.17152	0.21291	RANDOM	18.498

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
0.42		-0.11	-0.34		-0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.834
r_dihedral_angle_4_deg	16.922
r_dihedral_angle_3_deg	12.9
r_dihedral_angle_1_deg	5.163
r_scangle_it	3.324
r_scbond_it	2.119
r_angle_refined_deg	1.444
r_mcangle_it	1.221
r_mcbond_it	0.801
r_nbtor_refined	0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.834
r_dihedral_angle_4_deg	16.922
r_dihedral_angle_3_deg	12.9
r_dihedral_angle_1_deg	5.163
r_scangle_it	3.324
r_scbond_it	2.119
r_angle_refined_deg	1.444
r_mcangle_it	1.221
r_mcbond_it	0.801
r_nbtor_refined	0.3
r_nbd_refined	0.205
r_symmetry_vdw_refined	0.179
r_symmetry_hbond_refined	0.141
r_xyhbond_nbd_refined	0.122
r_chiral_restr	0.097
r_bond_refined_d	0.013
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3410
Nucleic Acid Atoms
Solvent Atoms	471
Heterogen Atoms	54

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing
ARP/wARP	model building

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.