2BMG | pdb_00002bmg

Crystal structure of factor Xa in complex with 50

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.7	298	PEG600, MES, CACL2, PH 5.7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57	α = 90
b = 72.3	β = 90
c = 78.1	γ = 90

Symmetry
Space Group	P 21 21 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	MARRESEARCH	OSMIC MIRRORS	2000-10-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	ELLIOTT GX-13

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	2.7	50	98	0.09	12	3.7		9120			20.4

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	2.7	2.8	84		0.22	5.4	2.7

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1LPG	2.7	50	9098	910		0.1934	0.2	0.2774	0.2	26.7

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]
-0.068			0.12		-0.052

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	24.8
c_scangle_it	11.2
c_mcangle_it	8.7
c_scbond_it	7.6
c_mcbond_it	5.4
c_angle_deg	1.3323
c_improper_angle_d	0.86
c_bond_d	0.00923
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2249
Nucleic Acid Atoms
Solvent Atoms	218
Heterogen Atoms	36

Software

Software
Software Name	Purpose
CNX	refinement
XDS	data reduction
XSCALE	data scaling
CNX	phasing