2A6A

Crystal structure of Glycoprotein endopeptidase (tm0874) from THERMOTOGA MARITIMA at 2.50 A resolution

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP	4	273	10.0% MPD, 0.1M Citrate pH 4.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 273K

Crystal Properties
Matthews coefficient	Solvent content
3.25	61.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.272	α = 90
b = 217.112	β = 90
c = 51.953	γ = 90

Symmetry
Space Group	C 2 2 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 315		2005-04-03	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.979413, 0.918370	SSRL	BL11-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.5	29.24	99.6	0.051	0.051	11.7	3.6		18685

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.64		99.9	0.469	0.469	1.6	3.7

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.5	29.24	17730	955	99.41	0.193	0.191	0.235	RANDOM	54.618

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]
-4.52			-1.12		5.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.512
r_dihedral_angle_4_deg	17.775
r_dihedral_angle_3_deg	16.74
r_scangle_it	7.846
r_dihedral_angle_1_deg	7.109
r_scbond_it	5.664
r_mcangle_it	3.352
r_mcbond_it	2.17
r_angle_refined_deg	1.688
r_angle_other_deg	0.852
r_mcbond_other	0.49
r_symmetry_hbond_refined	0.466
r_nbd_refined	0.227
r_xyhbond_nbd_refined	0.21
r_nbtor_refined	0.187
r_nbd_other	0.182
r_symmetry_vdw_refined	0.162
r_symmetry_vdw_other	0.16
r_chiral_restr	0.093
r_nbtor_other	0.088
r_bond_refined_d	0.018
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2860
Nucleic Acid Atoms
Solvent Atoms	22
Heterogen Atoms	7

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
CCP4	data scaling
SHELXD	phasing
autoSHARP	phasing