Experiment: 3ZYM

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1HF8	PDB ENTRY 1HF8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.2	289	CRYSTALS WERE GROWN IN SITTING DROPS CONTAINING EQUAL AMOUNTS (200-400 NL) OF PROTEIN (15 MG/ML IN 20 MM HEPES PH 7.4, 120 MM NACL, 4 MM DTT) AND RESERVOIR SOLUTION (100 MM PHOSPHATE-CITRATE PH 4.2, 200 MM NACL, 50% (V/V) PEG-200) AND EQUILIBRATED AGAINST 80 UL OF RESERVOIR SOLUTION AT 16C. CRYSTALS WERE CRYOPROTECTED BY BRIEF IMMERSION (5-60 S) IN RESERVOIR SOLUTION SUPPLEMENTED WITH 25% GLYCEROL AND WERE RAPIDLY CRYOCOOLED IN LIQUID N2 OR A 100 K STREAM OF N2 GAS.

Crystal Properties
Matthews coefficient	Solvent content
3.49	64.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 161.051	α = 90
b = 100.26	β = 118.88
c = 104.021	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 CCD	MIRRORS	2010-10-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03		Diamond	I03

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	91.1	99.7	0.08	10	3.7		93133		-3	33.81

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	99.8		0.73	1.9	3.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 1HF8	2.03	45.573	1.34	93104	4667	99.6	0.1815	0.1807	0.198	42.38

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]
1.0877		2.8613	-3.7334		2.6457

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	12.982
f_angle_d	0.913
f_chiral_restr	0.063
f_bond_d	0.008
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6713
Nucleic Acid Atoms
Solvent Atoms	473
Heterogen Atoms	71

Software

Software
Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	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 R01GM133198.