Experiment: 2PYW

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	10% PEG8000, 0.1M sodium cacodylate, 0.2M magnesium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.79	55.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 162.46	α = 90
b = 82.24	β = 117.83
c = 91.08	γ = 90

Symmetry
Space Group	C 1 2 1

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 4	mirrors	2003-08-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X8C	1.0	NSLS	X8C

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	1.9	80.58	98.7	0.045	16.9	3.38	83556	82470

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	1.9	1.97	90.8		0.175	4.8

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 2OLC	1.9	80.58	83556	78352	4105	98.66	0.16475	0.16475	0.16303	0.19723	RANDOM	17.312

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]
-0.4		-0.27	0.72		-0.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.042
r_dihedral_angle_4_deg	16.673
r_dihedral_angle_3_deg	11.901
r_dihedral_angle_1_deg	5.907
r_scangle_it	3.199
r_scbond_it	2.098
r_angle_refined_deg	1.38
r_mcangle_it	1.196
r_mcbond_it	0.819
r_symmetry_hbond_refined	0.317

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.042
r_dihedral_angle_4_deg	16.673
r_dihedral_angle_3_deg	11.901
r_dihedral_angle_1_deg	5.907
r_scangle_it	3.199
r_scbond_it	2.098
r_angle_refined_deg	1.38
r_mcangle_it	1.196
r_mcbond_it	0.819
r_symmetry_hbond_refined	0.317
r_nbtor_refined	0.303
r_symmetry_vdw_refined	0.214
r_nbd_refined	0.195
r_xyhbond_nbd_refined	0.132
r_chiral_restr	0.095
r_metal_ion_refined	0.068
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6650
Nucleic Acid Atoms
Solvent Atoms	778
Heterogen Atoms	103

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	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.