Experiment: 1WZV

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1C4Z	PDB ENTRY 1C4Z CHAIN D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.3	298	PEG 3350, calcium acetate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.4	49.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.231	α = 90
b = 35.486	β = 104.55
c = 92.58	γ = 90

Symmetry
Space Group	P 1 21 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	Bruker DIP-6040		2004-12-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.900	SPring-8	BL44XU

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	2.1	100	97.7	0.046	16.8	3.65		19900		-3	36.2

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)
	2.1	2.18	94.9		0.237

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1C4Z CHAIN D	2.1	20	18854	1011	97.76	0.20952	0.20952	0.20658	0.26726	RANDOM	37.989

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]
-1.48		0.28	2.03		-0.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.674
r_dihedral_angle_3_deg	15.725
r_dihedral_angle_4_deg	10.96
r_dihedral_angle_1_deg	5.124
r_scangle_it	3.595
r_scbond_it	2.194
r_mcangle_it	1.396
r_angle_refined_deg	1.325
r_mcbond_it	0.932
r_symmetry_vdw_refined	0.337

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.674
r_dihedral_angle_3_deg	15.725
r_dihedral_angle_4_deg	10.96
r_dihedral_angle_1_deg	5.124
r_scangle_it	3.595
r_scbond_it	2.194
r_mcangle_it	1.396
r_angle_refined_deg	1.325
r_mcbond_it	0.932
r_symmetry_vdw_refined	0.337
r_nbtor_refined	0.31
r_nbd_refined	0.193
r_xyhbond_nbd_refined	0.132
r_symmetry_hbond_refined	0.112
r_chiral_restr	0.08
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2454
Nucleic Acid Atoms
Solvent Atoms	138
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	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 R01GM157729.