Experiment: 3BIM

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1R29

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	298	75 mM NaAcetate, 900 mM K2HPO4, 700 NaH2PO4, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.87	68.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 150.55	α = 90
b = 150.55	β = 90
c = 312.25	γ = 120

Symmetry
Space Group	P 61 2 2

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 315		2004-12-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.979	APS	19-ID

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	2.6	48.7	97	0.07	20	12.3	65050	63099

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)
	2.6	2.72	98.5		0.54	5.3	12.3

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1R29	2.6	48.7	65050	63035	3069	97.06	0.221	0.219	0.26	RANDOM	71.704

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]
-1.62	-0.81		-1.62		2.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.1
r_dihedral_angle_4_deg	22.138
r_dihedral_angle_3_deg	20.349
r_dihedral_angle_1_deg	7.098
r_scangle_it	4.703
r_scbond_it	2.858
r_mcangle_it	2.275
r_angle_refined_deg	1.783
r_mcbond_it	1.629
r_nbtor_refined	0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.1
r_dihedral_angle_4_deg	22.138
r_dihedral_angle_3_deg	20.349
r_dihedral_angle_1_deg	7.098
r_scangle_it	4.703
r_scbond_it	2.858
r_mcangle_it	2.275
r_angle_refined_deg	1.783
r_mcbond_it	1.629
r_nbtor_refined	0.32
r_symmetry_vdw_refined	0.307
r_nbd_refined	0.25
r_symmetry_hbond_refined	0.249
r_xyhbond_nbd_refined	0.167
r_chiral_restr	0.119
r_bond_refined_d	0.018
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8950
Nucleic Acid Atoms
Solvent Atoms	141
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection

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.