4DDY | pdb_00004ddy

CTX-M-9 class A beta-lactamase complexed with compound 10

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3G35	pdb entry 3G35

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	292	Potassium Phosphate, pH 8.5, vapor diffusion, hanging drop, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2	38.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.014	α = 90
b = 107.105	β = 102.11
c = 47.509	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	ADSC QUANTUM 210	mirrors	2010-06-21		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X6A	0.9795	NSLS	X6A

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	1.36	50	98.9	0.06	17.9	3.7	93474	92455		5

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	1.36	1.38	92.7		0.517		3.1	4286

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	pdb entry 3G35	1.36	50	93474	92348	4625	98.68	0.1725	0.1708	0.169	0.205	0.2023	RANDOM	15.0039

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]
0.82		2.75	-1.51		1.85

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.942
r_dihedral_angle_3_deg	11.987
r_dihedral_angle_4_deg	10.72
r_dihedral_angle_1_deg	6.209
r_scangle_it	3.245
r_scbond_it	2.212
r_angle_refined_deg	1.656
r_mcangle_it	1.338
r_mcbond_it	0.87
r_rigid_bond_restr	0.74
r_chiral_restr	0.104
r_bond_refined_d	0.015
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3888
Nucleic Acid Atoms
Solvent Atoms	519
Heterogen Atoms	300

Software

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