1W8Y | pdb_00001w8y

Crystal structure of the nitrocefin acyl-DD-peptidase from Actinomadura R39.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1W79	PDB ENTRY 1W79

Crystallization

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.49	α = 90
b = 94.36	β = 94.58
c = 107.2	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	MARRESEARCH	MIRRORS	2004-03-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A		ESRF	BM30A

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	2.4	40.8	86.6	0.1	9.5	2.9		69694		2	42.1

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	2.4	2.53	80.5		0.54	2.2	2.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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 1W79	2.4	19.94	2	69453	3524	86.3	0.22	0.22	0.22	0.277	0.27	RANDOM	43.6

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]
-4.25		8.57	12.34		-8.08

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	24.2
c_scangle_it	2.53
c_mcangle_it	2.02
c_scbond_it	1.79
c_angle_deg	1.3
c_mcbond_it	1.23
c_improper_angle_d	0.84
c_bond_d	0.007
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13394
Nucleic Acid Atoms
Solvent Atoms	829
Heterogen Atoms	168

Software

Software
Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling