1HZ6 | pdb_00001hz6

CRYSTAL STRUCTURES OF THE B1 DOMAIN OF PROTEIN L FROM PEPTOSTREPTOCOCCUS MAGNUS WITH A TYROSINE TO TRYPTOPHAN SUBSTITUTION

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		C3 DOMAIN OF PROTEIN L (UNPUBLISHED: T. WAN AND B. SUTTON)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	277	30%PEG 8000, 0.2M Ammonium Sulfate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.75	54.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.611	α = 90
b = 54.02	β = 90
c = 95.069	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV	Mirrors	1999-10-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.7	25	96.3	0.074	0.08	17	4.94	120968	28825		-3	23.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.69	1.71	95.1		0.273	0.252	6.8	4.9	1031

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	C3 DOMAIN OF PROTEIN L (UNPUBLISHED: T. WAN AND B. SUTTON)	1.7	25	-3	29936	28825	1471	96.3	0.193	0.193	0.19	0.218	0.22	RANDOM	24.2

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]
0.55			1.1		-1.65

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	25.7
c_scangle_it	4.28
c_scbond_it	2.87
c_mcangle_it	2.48
c_mcbond_it	1.67
c_angle_deg	1.22
c_improper_angle_d	0.68
c_bond_d	0.0056

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1488
Nucleic Acid Atoms
Solvent Atoms	299
Heterogen Atoms

Software

Software
Software Name	Purpose
EPMR	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

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.