Experiment: 3BYD

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	296	25%(w/v) PEG 4000, 0.1M sodium acetate buffer, 0.2M ammonium sulfate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.545	α = 90
b = 73.431	β = 90
c = 84.561	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		2000-09-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I711	1.0292	MAX II	I711

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	1.93	56	96.9	0.052	14.8	4.6		21787			28.8

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	1.93	2	96.1		0.129		4.2	2091

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1BZA	1.93	55.47	22433	21754	1120	96.97	0.211	0.184	0.182	0.225	RANDOM	15.24

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]
0.59			0.04		-0.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.582
r_dihedral_angle_3_deg	11.751
r_dihedral_angle_4_deg	11.324
r_dihedral_angle_1_deg	5.487
r_scangle_it	2.514
r_scbond_it	1.717
r_angle_refined_deg	1.236
r_mcangle_it	0.923
r_mcbond_it	0.627
r_nbtor_refined	0.293

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.582
r_dihedral_angle_3_deg	11.751
r_dihedral_angle_4_deg	11.324
r_dihedral_angle_1_deg	5.487
r_scangle_it	2.514
r_scbond_it	1.717
r_angle_refined_deg	1.236
r_mcangle_it	0.923
r_mcbond_it	0.627
r_nbtor_refined	0.293
r_nbd_refined	0.199
r_symmetry_vdw_refined	0.151
r_symmetry_hbond_refined	0.144
r_xyhbond_nbd_refined	0.122
r_chiral_restr	0.076
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1941
Nucleic Acid Atoms
Solvent Atoms	203
Heterogen Atoms	24

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
HKL-2000	data scaling
CNS	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.