2ZQA | pdb_00002zqa

Cefotaxime acyl-intermediate structure of class a beta-lacta Toho-1 E166A/R274N/R276N triple mutant

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2ZQ7	PDB ENTRY 2ZQ7

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	53.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.522	α = 90
b = 72.522	β = 90
c = 97.96	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	2007-12-11	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	0.95	50	99.7	0.076	25.88	10.3		186625

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)
1	0.95	0.97	95.7		0.392	4.77	6.7

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 2ZQ7	0.95	50	177014	9369	99.67	0.13557	0.13507	0.14	0.14487	0.14	RANDOM	10.501

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]
-0.14	-0.07		-0.14		0.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.066
r_dihedral_angle_4_deg	12.815
r_dihedral_angle_3_deg	10.361
r_dihedral_angle_1_deg	6.469
r_sphericity_free	4.684
r_sphericity_bonded	4.155
r_scangle_it	3.072
r_scbond_it	2.153
r_mcangle_it	1.7
r_angle_refined_deg	1.539
r_mcbond_it	1.171
r_rigid_bond_restr	0.994
r_nbtor_refined	0.306
r_nbd_refined	0.206
r_symmetry_vdw_refined	0.17
r_symmetry_hbond_refined	0.127
r_xyhbond_nbd_refined	0.121
r_chiral_restr	0.088
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1966
Nucleic Acid Atoms
Solvent Atoms	391
Heterogen Atoms	46

Software

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