Experiment: 3GRB

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1F41	PDB entry 1f41

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	ZINC ACETATE 0.2 M, SODIUM CITRATE 0.1 M, AMMONIUM SULFATE 2,0M, PH 6.5; CRYSTALS WERE SOAKED IN MOTHER LIQUOR SUPPLEMENTED WITH 10 % GLYCEROL BEFORE FREEZING IN LIQUID NITROGEN, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.8	α = 90
b = 62.197	β = 89.99
c = 47.347	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 225 mm CCD		2008-09-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE W01B-MX2	1.458	LNLS	W01B-MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.75	25.48	99.4	0.063	21.8	7.2		54923			26.45

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.75	1.79	99.16		0.383	4	7	7876

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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 1f41	1.75	25.48	46093	2882	99.47	0.206	0.20626	0.20293	0.25961	RANDOM	30.394

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]
1.06		0.09	0.11		-1.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.092
r_dihedral_angle_3_deg	16.933
r_dihedral_angle_4_deg	16.783
r_dihedral_angle_1_deg	7.191
r_sphericity_free	6.984
r_sphericity_bonded	4.936
r_scangle_it	4.48
r_scbond_it	3.016
r_mcangle_it	2.352
r_rigid_bond_restr	1.849

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.092
r_dihedral_angle_3_deg	16.933
r_dihedral_angle_4_deg	16.783
r_dihedral_angle_1_deg	7.191
r_sphericity_free	6.984
r_sphericity_bonded	4.936
r_scangle_it	4.48
r_scbond_it	3.016
r_mcangle_it	2.352
r_rigid_bond_restr	1.849
r_angle_refined_deg	1.679
r_mcbond_it	1.427
r_chiral_restr	0.124
r_bond_refined_d	0.015
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3551
Nucleic Acid Atoms
Solvent Atoms	285
Heterogen Atoms	78

Software

Software
Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	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 R01GM133198.