Experiment: 3GMM

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3GML	PDB entry 3GML

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	295	0.2 M Malonate pH 4.5, 20%(v/v) PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.74	α = 90
b = 97.9	β = 106.57
c = 55.42	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	CCD	MARMOSAIC 325 mm CCD	flat mirror	2007-11-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.9795	SSRL	BL11-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.8	30	99.4	0.043	17.2	3.8	39342	39342		-3	34

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.9	99.3		0.489	2.8	3.8	5893

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 3GML	1.8	29.77	39341	37348	1993	99.55	0.17674	0.17674	0.17458	0.18	0.21874	0.23	RANDOM	25.624

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]
-1.83		-1.47	1.96		-0.97

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.427
r_dihedral_angle_4_deg	20.003
r_dihedral_angle_3_deg	15.081
r_dihedral_angle_1_deg	6.61
r_scangle_it	5.163
r_scbond_it	3.389
r_mcangle_it	2.175
r_angle_refined_deg	2.144
r_mcbond_it	1.321
r_chiral_restr	0.156

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.427
r_dihedral_angle_4_deg	20.003
r_dihedral_angle_3_deg	15.081
r_dihedral_angle_1_deg	6.61
r_scangle_it	5.163
r_scbond_it	3.389
r_mcangle_it	2.175
r_angle_refined_deg	2.144
r_mcbond_it	1.321
r_chiral_restr	0.156
r_bond_refined_d	0.023
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2975
Nucleic Acid Atoms
Solvent Atoms	314
Heterogen Atoms	228

Software

Software
Software Name	Purpose
MAR345	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

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.