5Z03 | pdb_00005z03

Mutant (S106A) Escherichia coli L,D-carboxypeptidase A (LdcA)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.02M Tris Cl pH 8.5, 0.2M sodium thiocyanate, 12% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.02	38.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.823	α = 90
b = 93.379	β = 90
c = 86.793	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 300K		2016-12-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	0.98	Photon Factory	BL-17A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	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	1.75	46.7	99.1	0.097	0.057	0.999	11.2	6.5		56189

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.77	85		0.832	0.368	0.491	2	5.5

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-Factor (All)	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	1.755	46.689	56144	2765	99.105	0.229	0.2274	0.24	0.2691	0.27	RANDOM	32.487

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]
3.709			-2.707		-1.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.909
r_dihedral_angle_4_deg	21.093
r_dihedral_angle_3_deg	14.405
r_lrange_it	7.406
r_lrange_other	7.405
r_dihedral_angle_1_deg	6.956
r_scangle_it	5.616
r_scangle_other	5.615
r_mcangle_it	4.185
r_mcangle_other	4.184
r_scbond_it	3.662
r_scbond_other	3.662
r_mcbond_it	2.89
r_mcbond_other	2.89
r_angle_refined_deg	1.902
r_angle_other_deg	1.081
r_symmetry_xyhbond_nbd_refined	0.304
r_nbd_other	0.268
r_xyhbond_nbd_other	0.251
r_symmetry_nbd_refined	0.248
r_nbd_refined	0.207
r_xyhbond_nbd_refined	0.182
r_nbtor_refined	0.176
r_symmetry_nbd_other	0.167
r_chiral_restr	0.116
r_symmetry_nbtor_other	0.082
r_symmetry_xyhbond_nbd_other	0.047
r_bond_refined_d	0.019
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4429
Nucleic Acid Atoms
Solvent Atoms	56
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing