Experiment: 2GNQ

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VYH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	300	20%peg5k mme, bis-tris 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.045	α = 90
b = 55.323	β = 90
c = 124.308	γ = 90

Symmetry
Space Group	P 21 21 21

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 V		2006-03-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.8	62.14	93			30580	30580

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.8	1.86	62.7

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	1VYH	1.8	62.14	29046	29046	1544	93.23	0.151	0.151	0.149	0.192	RANDOM	14.759

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]
-0.17			0.49		-0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.601
r_dihedral_angle_4_deg	13.691
r_dihedral_angle_3_deg	12.188
r_dihedral_angle_1_deg	7.152
r_scangle_it	2.937
r_scbond_it	1.824
r_angle_refined_deg	1.277
r_mcangle_it	1.036
r_mcbond_it	0.628
r_nbtor_refined	0.296

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.601
r_dihedral_angle_4_deg	13.691
r_dihedral_angle_3_deg	12.188
r_dihedral_angle_1_deg	7.152
r_scangle_it	2.937
r_scbond_it	1.824
r_angle_refined_deg	1.277
r_mcangle_it	1.036
r_mcbond_it	0.628
r_nbtor_refined	0.296
r_symmetry_vdw_refined	0.196
r_nbd_refined	0.195
r_xyhbond_nbd_refined	0.127
r_symmetry_hbond_refined	0.127
r_chiral_restr	0.093
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2485
Nucleic Acid Atoms
Solvent Atoms	484
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
HKL-2000	data scaling
MOLREP	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.