Experiment: 3RNZ

Crystal structure of Bacillus Amyloliquefaciens Pyroglutamyl Peptidase I

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1AUG	PDB entry 1AUG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.9	298	1.8M sodium phosphate monobasic monohydrate, potassium phosphate dibasic, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 289.89	α = 90
b = 45.36	β = 91.34
c = 68.09	γ = 90

Symmetry
Space Group	C 1 2 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	RIGAKU RAXIS HTC	mirrors	2010-03-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.54

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	2.01	25	99.6	0.035	32.9	4.2	59489	59251		5

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	2.01	2.04	98.6		0.138	8.4	4	2926

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 1AUG	2.01	25	61430	58470	2960	95.2	0.176	0.176	0.174	0.1743	0.209	0.2096	RANDOM	22.337

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]
4.462		0.174	-5.781		1.319

RMS Deviations
Key	Refinement Restraint Deviation
c_scangle_it	3.159
c_scbond_it	2.262
c_mcangle_it	1.967
c_angle_deg	1.84
c_mcbond_it	1.347
c_bond_d	0.019

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6337
Nucleic Acid Atoms
Solvent Atoms	437
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling