Experiment: 1ZD0

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	modified microbatch	7.7	293	Magnesium Acetate and PEG 3350, pH 7.7, modified microbatch, temperature 293K
2	modified microbatch	7.7	293	Magnesium Acetate, Methanol, and PEG 3350, pH 7.7, modified microbatch, temperature 293K
3	modified microbatch	7.7	293	Magnesium Acetate, Methanol, and PEG 3350, pH 7.7, modified microbatch, temperature 293K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.46	α = 90
b = 53.46	β = 90
c = 85.7	γ = 120

Symmetry
Space Group	P 31 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	MARRESEARCH		2004-12-17		SINGLE WAVELENGTH
2	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV		2005-01-05		SINGLE WAVELENGTH
3	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV		2005-03-04		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.97	APS	22-ID
2	ROTATING ANODE	RIGAKU MICROMAX-007	2.29
3	ROTATING ANODE	RIGAKU FR-D	2.29

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
1,2,3	1.7	50	98.1	0.045		9.5		15870

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)
	1.7	1.76	85.1		0.21		4.3	1344

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-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAS	THROUGHOUT	1.7	46.27	15838	797	98.15	0.205	0.202	0.252	RANDOM	30.738

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]
-0.13	-0.07		-0.13		0.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	46.929
r_dihedral_angle_4_deg	20.471
r_dihedral_angle_3_deg	14.45
r_dihedral_angle_1_deg	6.24
r_scangle_it	3.01
r_scbond_it	2.129
r_mcangle_it	1.47
r_angle_refined_deg	1.422
r_mcbond_it	0.981
r_nbtor_refined	0.304

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	46.929
r_dihedral_angle_4_deg	20.471
r_dihedral_angle_3_deg	14.45
r_dihedral_angle_1_deg	6.24
r_scangle_it	3.01
r_scbond_it	2.129
r_mcangle_it	1.47
r_angle_refined_deg	1.422
r_mcbond_it	0.981
r_nbtor_refined	0.304
r_symmetry_vdw_refined	0.276
r_nbd_refined	0.233
r_xyhbond_nbd_refined	0.151
r_symmetry_hbond_refined	0.114
r_chiral_restr	0.1
r_metal_ion_refined	0.027
r_bond_refined_d	0.016
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1074
Nucleic Acid Atoms
Solvent Atoms	93
Heterogen Atoms	20

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement

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.