Experiment: 2AMY

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	277	10 MG/ML PROTEIN, 24 % W/V PEG 2K, 0.12 M GLYCINE, 0.1 M TRIETHANOLAMINE, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
2	VAPOR DIFFUSION, HANGING DROP	8.5	277	10 MG/ML PROTEIN, 24 % W/V PEG 2K, 0.12 M GLYCINE, 0.1 M TRIETHANOLAMINE, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.6	51.9
2.6	51.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.622	α = 90
b = 70.622	β = 90
c = 100.15	γ = 120

Symmetry
Space Group	P 32 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	MARMOSAIC 225 mm CCD	HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR	2005-07-11	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	MARMOSAIC 300 mm CCD	HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR	2005-06-13	M	MAD
3	1
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	0.97243	APS	22-BM
2	SYNCHROTRON	APS BEAMLINE 22-ID	0.97625, 0.97947	APS	22-ID

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	2.09	50	99	0.069	20.356	12.3		17547

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	2.09	2.16	91.5	91.5	0.599	3.031	7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	MAD	THROUGHOUT	2.09	38.745	17514	924	99.49	0.202	0.20226	0.199	0.272	RANDOM	56.423

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]
0.79	0.39		0.79		-1.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.427
r_dihedral_angle_3_deg	17.162
r_dihedral_angle_4_deg	15.44
r_dihedral_angle_1_deg	6.85
r_scangle_it	6.65
r_scbond_it	5.216
r_mcangle_it	3.005
r_mcbond_it	1.838
r_angle_refined_deg	1.821
r_nbtor_refined	0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.427
r_dihedral_angle_3_deg	17.162
r_dihedral_angle_4_deg	15.44
r_dihedral_angle_1_deg	6.85
r_scangle_it	6.65
r_scbond_it	5.216
r_mcangle_it	3.005
r_mcbond_it	1.838
r_angle_refined_deg	1.821
r_nbtor_refined	0.31
r_symmetry_vdw_refined	0.246
r_nbd_refined	0.224
r_xyhbond_nbd_refined	0.203
r_symmetry_hbond_refined	0.203
r_chiral_restr	0.135
r_bond_refined_d	0.022
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1943
Nucleic Acid Atoms
Solvent Atoms	142
Heterogen Atoms	19

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SOLOMON	phasing
ARP/wARP	model building

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.