1HZ5 | pdb_00001hz5

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
experimental model	PDB	1HZ6	CRYSTAL STRUCTURE OF B1 DOMAIN (Y47W), NON -HIS-TAG COORDINATE STRUCTURE (SEE 1HZ6)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	277	0.2M Zinc Accetate and MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
4.31	71.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.437	α = 90
b = 66.437	β = 90
c = 109.181	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	IMAGE PLATE	RIGAKU RAXIS IV	mirrors	2000-05-10	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	1.8	30	99.8	0.066	0.065	18.5	4.4	116074	26449		-3	15.8

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	1.8	1.84	98		0.28	0.263	3.7	4.4	1696

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 (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	CRYSTAL STRUCTURE OF B1 DOMAIN (Y47W), NON -HIS-TAG COORDINATE STRUCTURE (SEE 1HZ6)	1.8	24.66	26468	26449	1341	99.9	0.188	0.188	0.19	0.193	0.19	RANDOM	20.9

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]
0.61	0.47		0.61		-1.22

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	26
c_scangle_it	3.33
c_scbond_it	2.43
c_mcangle_it	1.72
c_angle_deg	1.3
c_mcbond_it	1.13
c_improper_angle_d	0.69
c_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1132
Nucleic Acid Atoms
Solvent Atoms	237
Heterogen Atoms	10

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.