Experiment: 3BUP

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	Tris, NaCl, PEG6000, MPD. Crystal soaked in PNP-mannose at 4C, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.67	α = 90
b = 109.486	β = 90
c = 138.584	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	IMAGE PLATE	MAR scanner 345 mm plate	Osmic mirrors	2002-06-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

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	2.03	20	96	0.068	11.6	7.8	69044	66283

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	2.03	2.08	79.8		0.344	4.1	3	3614

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	PDB entry 1HTY	2.03	19.79	68416	66227	2347	96.81	0.154	0.152	0.195	RANDOM	19.27

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]
-0.04			-0.01		0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.474
r_dihedral_angle_4_deg	17.174
r_dihedral_angle_3_deg	13.116
r_dihedral_angle_1_deg	6.233
r_scangle_it	2.844
r_scbond_it	1.893
r_angle_refined_deg	1.344
r_mcangle_it	1.134
r_mcbond_it	0.745
r_nbtor_refined	0.306

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.474
r_dihedral_angle_4_deg	17.174
r_dihedral_angle_3_deg	13.116
r_dihedral_angle_1_deg	6.233
r_scangle_it	2.844
r_scbond_it	1.893
r_angle_refined_deg	1.344
r_mcangle_it	1.134
r_mcbond_it	0.745
r_nbtor_refined	0.306
r_symmetry_vdw_refined	0.241
r_nbd_refined	0.203
r_xyhbond_nbd_refined	0.153
r_symmetry_hbond_refined	0.144
r_chiral_restr	0.095
r_bond_refined_d	0.013
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8187
Nucleic Acid Atoms
Solvent Atoms	1105
Heterogen Atoms	35

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
CNS	refinement
DENZO	data reduction
PDB_EXTRACT	data extraction
MAR345dtb	data collection
CNS	phasing

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.