3AK5 | pdb_00003ak5

Hemoglobin protease (Hbp) passenger missing domain-2

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	293	9% PEG 1000, 10% PEG 8000, 0.1M NaOAc pH 5.0, 20% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
3.05	59.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 292.803	α = 90
b = 53.936	β = 107.32
c = 335.953	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	CCD	ADSC QUANTUM 315		2005-05-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.000	SPring-8	BL41XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.2	50	93		3.69		239062		2

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)
	2.2	2.28	71.9		0.213		2.5	11129

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 (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 1WXR	2.2	48.56	227076	11985	100	0.2282	0.2255	0.2255	0.22	0.2801	0.28	RANDOM	32.732

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]
-1.49		-2.3	2.06		-1.94

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.74
r_dihedral_angle_4_deg	20.883
r_dihedral_angle_3_deg	18.061
r_dihedral_angle_1_deg	7.777
r_scangle_it	4.056
r_scbond_it	2.592
r_angle_refined_deg	1.949
r_mcangle_it	1.672
r_mcbond_it	0.932
r_chiral_restr	0.134
r_bond_refined_d	0.021
r_gen_planes_refined	0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	28813
Nucleic Acid Atoms
Solvent Atoms	1485
Heterogen Atoms	4

Software

Software
Software Name	Purpose
ADSC	data collection
EPMR	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling