2ZQ7 | pdb_00002zq7

Apo structure of Class A beta-lactamase Toho-1 E166A/R274N/R276N triple mutant

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	298	1.95-2.10M Ammonium sulfate, 0.2M sodium citrate, pH5.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.545	α = 90
b = 72.545	β = 90
c = 97.656	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 V	mirrors	2007-12-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B1	0.8	SPring-8	BL26B1

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	0.94	50	99.9	0.075	25.99	10.1		192768

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)
	0.94	0.96	98.9		0.384	4.32	5.7

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	PDB ENTRY 1IYO	0.94	50	182648	9670	99.92	0.1358	0.13519	0.14	0.14726	0.15	RANDOM	10.475

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]
-0.23	-0.12		-0.23		0.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.841
r_dihedral_angle_4_deg	13.007
r_dihedral_angle_3_deg	10.695
r_dihedral_angle_1_deg	6.354
r_sphericity_free	5.02
r_sphericity_bonded	4.634
r_scangle_it	3.159
r_scbond_it	2.314
r_mcangle_it	1.847
r_angle_refined_deg	1.495
r_mcbond_it	1.285
r_rigid_bond_restr	1.049
r_nbtor_refined	0.307
r_nbd_refined	0.207
r_symmetry_vdw_refined	0.176
r_xyhbond_nbd_refined	0.115
r_symmetry_hbond_refined	0.109
r_chiral_restr	0.093
r_bond_refined_d	0.01
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2267
Nucleic Acid Atoms
Solvent Atoms	511
Heterogen Atoms	30

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling