5PAA

Crystal Structure of Factor VIIa in complex with cyclohexylmethanamine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		inhouse model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277	16 mg/ml protein in 20mM Tris/HCl pH 8.4, 5 mM benzamidine, 0.1 M NaCl, 50 mM CaCl2 mixed 1+1 with 32-35% AMMONIUM SULPHATE, 2% PEG 4000, 0.1 M Bicine-NaOH pH 8.5, 15% glycerol

Crystal Properties
Matthews coefficient	Solvent content
3.76	67.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.298	α = 90
b = 95.298	β = 90
c = 116.041	γ = 90

Symmetry
Space Group	P 41 21 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	IMAGE PLATE	MAR scanner 345 mm plate		2007-04-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.5419

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	1.98	50	98.1	0.128	7.3	6.9		37204

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	1.98	2.05	81.5		0.912		3.7	3013

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	inhouse model	1.98	47.67	30785	1622	85.92	0.186	0.1846	0.2145	RANDOM	30.461

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]
-0.53			-0.53		1.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.058
r_dihedral_angle_4_deg	17.605
r_dihedral_angle_3_deg	14.807
r_dihedral_angle_1_deg	6.244
r_scangle_it	2.689
r_scbond_it	1.748
r_mcangle_it	1.453
r_angle_refined_deg	1.296
r_mcbond_it	0.936
r_angle_other_deg	0.872
r_symmetry_vdw_other	0.204
r_nbd_other	0.202
r_nbd_refined	0.188
r_nbtor_refined	0.173
r_xyhbond_nbd_refined	0.169
r_mcbond_other	0.157
r_symmetry_hbond_refined	0.143
r_nbtor_other	0.082
r_chiral_restr	0.076
r_metal_ion_refined	0.062
r_symmetry_vdw_refined	0.052
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2376
Nucleic Acid Atoms
Solvent Atoms	289
Heterogen Atoms	40

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing