Experiment: 2BDB

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	294	25MM SODIUM SULPHATE, 25MM SODIUM ACETATE (PH 5.0), 25 MG/ML PPE AND 17.5 MG/ML NPI, AND THEN SOAKED WITH Ala-Ala (2 MG) IN 250MM SODIUM ACETATE (PH 5.0) (5 MICROLITRES) FOR 30 MIN, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.463	α = 90
b = 57.663	β = 90
c = 74.233	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	127	IMAGE PLATE	RIGAKU RAXIS IV	OSMIC MIRRORS	2005-06-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007

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	1.7	17.46	99.9	0.034	24.8	3.6		24480			16.3

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	1.7	1.79	99.9		0.144	8.2	3.5	3493

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	3EST	1.7	17.46	24480	24434	1245	99.84	0.165	0.165	0.163	0.17	0.194	0.2	RANDOM	17.222

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]
0.07			-0.42		0.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.705
r_dihedral_angle_4_deg	23.958
r_dihedral_angle_3_deg	11.371
r_dihedral_angle_1_deg	5.673
r_scangle_it	5.203
r_scbond_it	4.108
r_mcangle_it	2.872
r_mcbond_it	2.024
r_angle_refined_deg	1.371
r_nbtor_refined	0.307

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.705
r_dihedral_angle_4_deg	23.958
r_dihedral_angle_3_deg	11.371
r_dihedral_angle_1_deg	5.673
r_scangle_it	5.203
r_scbond_it	4.108
r_mcangle_it	2.872
r_mcbond_it	2.024
r_angle_refined_deg	1.371
r_nbtor_refined	0.307
r_symmetry_vdw_refined	0.222
r_nbd_refined	0.202
r_symmetry_hbond_refined	0.166
r_xyhbond_nbd_refined	0.116
r_chiral_restr	0.109
r_metal_ion_refined	0.104
r_bond_refined_d	0.013
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1802
Nucleic Acid Atoms
Solvent Atoms	126
Heterogen Atoms	17

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	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.