Experiment: 3GAD

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	hanging drop	4.6	289	2.5M Ammonium sulfate, 0.1M Sodium acetate trihydrate pH4.6, hanging drop, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
3.24	62.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.88	α = 90
b = 98.94	β = 90
c = 108.58	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	CCD	MAR CCD 165 mm		2008-02-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BSRF BEAMLINE 3W1A	1.0	BSRF	3W1A

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	1.8	35.51	98	0.038				92291		-3	24.511

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	1.8	1.9	97.3		0.219	7.5

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1MFI	1.8	34.07	92282	2818	98.01	0.177	0.176	0.209	RANDOM	19.505

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]
0.06			0.09		-0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.994
r_dihedral_angle_4_deg	16.882
r_dihedral_angle_3_deg	12.859
r_dihedral_angle_1_deg	5.2
r_scangle_it	2.449
r_scbond_it	1.593
r_angle_refined_deg	1.102
r_mcangle_it	0.804
r_mcbond_it	0.51
r_nbtor_refined	0.304

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.994
r_dihedral_angle_4_deg	16.882
r_dihedral_angle_3_deg	12.859
r_dihedral_angle_1_deg	5.2
r_scangle_it	2.449
r_scbond_it	1.593
r_angle_refined_deg	1.102
r_mcangle_it	0.804
r_mcbond_it	0.51
r_nbtor_refined	0.304
r_symmetry_hbond_refined	0.224
r_nbd_refined	0.194
r_symmetry_vdw_refined	0.163
r_xyhbond_nbd_refined	0.13
r_chiral_restr	0.085
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5389
Nucleic Acid Atoms
Solvent Atoms	886
Heterogen Atoms	46

Software

Software
Software Name	Purpose
XSCALE	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 R01GM133198.