1GM7 | pdb_00001gm7

Crystal structures of penicillin acylase enzyme-substrate complexes: Structural insights into the catalytic mechanism

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		pH 7.50

Crystal Properties
Matthews coefficient	Solvent content
2.43	42.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.6	α = 90
b = 131.8	β = 105.6
c = 63.9	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	IMAGE PLATE	MAR scanner 300 mm plate			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7B		EMBL/DESY, HAMBURG	BW7B

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	1.45	30	99.6	0.061	18.7	3.4		144035			13.4

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	1.45	1.47	99.9		0.339	3.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	OTHER	THROUGHOUT	1.45	30	139473	4323	99.6	0.145	0.1546	0.173	0.169	RANDOM	14.8

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]

RMS Deviations
Key	Refinement Restraint Deviation
p_transverse_tor	28.1
p_special_tor	15
p_staggered_tor	13.3
p_scangle_it	4.964
p_planar_tor	4.7
p_scbond_it	3.735
p_mcangle_it	2.139
p_mcbond_it	1.647
p_multtor_nbd	0.263
p_singtor_nbd	0.162
p_xyhbond_nbd	0.149
p_chiral_restr	0.139
p_planar_d	0.041
p_angle_d	0.034
p_plane_restr	0.0267
p_bond_d	0.019
p_angle_deg
p_hb_or_metal_coord
p_xhyhbond_nbd
p_orthonormal_tor

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6075
Nucleic Acid Atoms
Solvent Atoms	930
Heterogen Atoms	104

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling