4IHM | pdb_00004ihm

G215S, A251G, T257A, D260G, T262D mutant of carboxypeptidase T from Thermoactinomyces vulgaris

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3QNV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	COUNTER-DIFFUSION			COUNTER DIFFUSION

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 158.101	α = 90
b = 158.101	β = 90
c = 104.584	γ = 120

Symmetry
Space Group	P 63 2 2

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				M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	0.8	SPring-8	BL41XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.29						191107

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 (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	3QNV	1.29	10	178446	9366	98.24	0.14079	0.14039	0.14	0.14821	0.15	RANDOM	15.097

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]
-0.02	-0.02		-0.02		0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.799
r_sphericity_free	27.458
r_dihedral_angle_4_deg	14.576
r_dihedral_angle_3_deg	11.365
r_rigid_bond_restr	9.483
r_sphericity_bonded	6.705
r_dihedral_angle_1_deg	6.142
r_angle_other_deg	3.731
r_angle_refined_deg	1.27
r_chiral_restr	0.082

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.799
r_sphericity_free	27.458
r_dihedral_angle_4_deg	14.576
r_dihedral_angle_3_deg	11.365
r_rigid_bond_restr	9.483
r_sphericity_bonded	6.705
r_dihedral_angle_1_deg	6.142
r_angle_other_deg	3.731
r_angle_refined_deg	1.27
r_chiral_restr	0.082
r_bond_refined_d	0.007
r_gen_planes_other	0.007
r_gen_planes_refined	0.006
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2577
Nucleic Acid Atoms
Solvent Atoms	395
Heterogen Atoms	68

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	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.