Experiment: 1ZMV

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Y8G	PDB ENTRY 1Y8G

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	PEG3350, Ammonium Sulphate, BIS-TRIS, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.82	56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.191	α = 90
b = 121.191	β = 90
c = 99.66	γ = 120

Symmetry
Space Group	P 61

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		2004-07-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13	0.8043	EMBL/DESY, HAMBURG	X13

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	3.105	51.78	98.2	0.109	14		14813	14813

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.105	3.15	99.3		2

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 1Y8G	3.105	51.78	14814	14814	740	98.2	0.20235	0.20235	0.19983	0.25108	RANDOM	68.393

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]
0.35	0.17		0.35		-0.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.21
r_dihedral_angle_3_deg	21.516
r_dihedral_angle_4_deg	19.398
r_dihedral_angle_1_deg	7.57
r_angle_refined_deg	1.955
r_symmetry_hbond_refined	0.395
r_nbtor_refined	0.342
r_nbd_refined	0.269
r_symmetry_vdw_refined	0.222
r_xyhbond_nbd_refined	0.151

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.21
r_dihedral_angle_3_deg	21.516
r_dihedral_angle_4_deg	19.398
r_dihedral_angle_1_deg	7.57
r_angle_refined_deg	1.955
r_symmetry_hbond_refined	0.395
r_nbtor_refined	0.342
r_nbd_refined	0.269
r_symmetry_vdw_refined	0.222
r_xyhbond_nbd_refined	0.151
r_chiral_restr	0.114
r_bond_refined_d	0.022
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4667
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement

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 R01GM157729.