Experiment: 3D32

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5.9	285	30 % (w/v) PEG3350 800 mM NaCl 50 mM MES, pH 5.9, VAPOR DIFFUSION, temperature 285K

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 129.287	α = 90
b = 35.415	β = 100.59
c = 58.209	γ = 90

Symmetry
Space Group	C 1 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	CCD	ADSC QUANTUM 4	monochromators, mirrors	2006-11-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.934	ESRF	ID14-1

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	1.3	63.5	93.9	0.041	0.041	16.3	2.1	60022	60022			12.1

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	1.3	1.37	92.3		0.32	0.32	2.7	2.2	8554

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1GNU	1.3	27.17	60022	60022	3070	93.9	0.178	0.178	0.177	0.18	0.195	0.2	SHELLS	10.922

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]
-0.38		0.19	0.65		-0.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.061
r_dihedral_angle_4_deg	14.17
r_dihedral_angle_3_deg	12.964
r_dihedral_angle_1_deg	6.326
r_scangle_it	2.244
r_scbond_it	1.639
r_angle_refined_deg	1.3
r_mcangle_it	1.013
r_mcbond_it	0.61
r_chiral_restr	0.091

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.061
r_dihedral_angle_4_deg	14.17
r_dihedral_angle_3_deg	12.964
r_dihedral_angle_1_deg	6.326
r_scangle_it	2.244
r_scbond_it	1.639
r_angle_refined_deg	1.3
r_mcangle_it	1.013
r_mcbond_it	0.61
r_chiral_restr	0.091
r_gen_planes_refined	0.006
r_bond_refined_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2160
Nucleic Acid Atoms
Solvent Atoms	301
Heterogen Atoms	11

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.