2FG0 | pdb_00002fg0

Crystal structure of a putative gamma-d-glutamyl-l-diamino acid endopeptidase (npun_r0659) from nostoc punctiforme pcc 73102 at 1.79 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5	277	1.4M Na3Citrate, 0.1M HEPES, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K, pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
3.43	63.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 125.08	α = 90
b = 125.08	β = 90
c = 97.67	γ = 90

Symmetry
Space Group	P 41 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	CCD	ADSC QUANTUM 210		2005-09-28	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1	1.0163, 0.9798	ALS	8.2.1

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	1.79	29.48	97.5	0.147	12.56	7.4		72488

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	1.79	1.86	89.4	89.4	0.01146	2.13	6.5

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	MAD	THROUGHOUT	1.79	29.48	68770	3659	99.55	0.155	0.154	0.17	0.172	0.19	RANDOM	22.209

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]
0.37			0.37		-0.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.222
r_dihedral_angle_4_deg	14.612
r_dihedral_angle_3_deg	12.46
r_scangle_it	6.639
r_dihedral_angle_1_deg	5.661
r_scbond_it	5.072
r_mcangle_it	2.896
r_mcbond_it	2.06
r_angle_refined_deg	1.513
r_angle_other_deg	0.891
r_mcbond_other	0.495
r_symmetry_vdw_other	0.267
r_symmetry_vdw_refined	0.224
r_nbd_refined	0.214
r_nbtor_refined	0.192
r_nbd_other	0.185
r_symmetry_hbond_refined	0.161
r_xyhbond_nbd_refined	0.16
r_chiral_restr	0.094
r_nbtor_other	0.091
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3426
Nucleic Acid Atoms
Solvent Atoms	428
Heterogen Atoms	18

Software

Software
Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SOLVE	phasing