Experiment: 1KQ9

Human methionine aminopeptidase type II in complex with L-methionine

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BN5	PDB ENTRY 1BN5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	277	18-23% t-butanol in 70 mM sodium citrate buffer, pH 5.3 to 5.6, 3 mM DTT (DL-dithiothreitol), VAPOR DIFFUSION, SITTING DROP at 277K, pH 5.5

Crystal Properties
Matthews coefficient	Solvent content
2.73	42.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.069	α = 90
b = 98.66	β = 90
c = 101.37	γ = 90

Symmetry
Space Group	C 2 2 21

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 4			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C		APS	14-BM-C

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	1.9	66	94	0.042	23.24	3.24		33600		3	21.07

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)
	1.9	1.97	96.5		0.046			3411

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 1BN5	1.9	66	31888	1701	93.7	0.1794	0.17792	0.1859	0.20663	0.2161	RANDOM	24.303

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]
1			-0.87		-0.14

RMS Deviations
Key	Refinement Restraint Deviation
p_scangle_it	5.323
p_mcangle_it	4.119
p_scbond_it	3.656
p_mcbond_it	3.087
p_angle_d	1.914
p_angle_deg	1.914
p_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2722
Nucleic Acid Atoms
Solvent Atoms	209
Heterogen Atoms	11

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
CCP4	data scaling