Experiment: 3GVQ

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	298	CITRATE BUFFER, PH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.145	α = 90
b = 103.145	β = 90
c = 71.287	γ = 120

Symmetry
Space Group	P 31 2 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		2003-09-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

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	2.1	30	98	0.07	0.07	9.9	4.5	25394	25394

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)
	2.1	2.18	86.3		0.4	0.4	2.2		2197

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MR	THROUGHOUT	PDB entry 1uro	2.1	30	24075	24075	1298	97.99	0.19517	0.19517	0.19261	0.19	0.24411	0.25	RANDOM	40.231

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]
-2.17	-1.09		-2.17		3.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.652
r_dihedral_angle_4_deg	16.054
r_dihedral_angle_3_deg	15.569
r_dihedral_angle_1_deg	5.534
r_scangle_it	3.273
r_scbond_it	2.032
r_mcangle_it	1.536
r_angle_refined_deg	1.265
r_mcbond_it	0.908
r_nbtor_refined	0.305

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.652
r_dihedral_angle_4_deg	16.054
r_dihedral_angle_3_deg	15.569
r_dihedral_angle_1_deg	5.534
r_scangle_it	3.273
r_scbond_it	2.032
r_mcangle_it	1.536
r_angle_refined_deg	1.265
r_mcbond_it	0.908
r_nbtor_refined	0.305
r_nbd_refined	0.206
r_symmetry_vdw_refined	0.153
r_xyhbond_nbd_refined	0.14
r_symmetry_hbond_refined	0.117
r_chiral_restr	0.087
r_bond_refined_d	0.013
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2805
Nucleic Acid Atoms
Solvent Atoms	145
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	phasing

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 R01GM157729.